| Next changeset 1:19ed3e4528c8 (2017-12-07) |
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SeqSero/LICENSE SeqSero/README.md SeqSero/SeqSero.py SeqSero/database/FliC_Family_b,d,j_special_genes.fasta SeqSero/database/FliC_Family_fg_special.fasta SeqSero/database/FliC_Family_g_special_genes.fasta SeqSero/database/FliC_Family_k,z_special_genes.fasta SeqSero/database/FliC_Family_k_z58_special_genes.fasta SeqSero/database/FliC_Family_l,v_special_genes.fasta SeqSero/database/FliC_Family_r,i_special_genes_short.fasta SeqSero/database/FliC_Family_z36z38_special_genes.fasta SeqSero/database/FliC_Family_z44_k_special_genes.fasta SeqSero/database/FliC_Family_z4z23_special_genes.fasta SeqSero/database/FliC_f_g_s_whole.fasta SeqSero/database/FljB_1_2_7_whole.fasta SeqSero/database/FljB_1_2_7_whole.fasta.amb SeqSero/database/FljB_1_2_7_whole.fasta.ann SeqSero/database/FljB_1_2_7_whole.fasta.bwt SeqSero/database/FljB_1_2_7_whole.fasta.pac SeqSero/database/FljB_1_2_7_whole.fasta.sa SeqSero/database/FljB_Family_1_special_genes_all.fasta SeqSero/database/FljB_Family_e_special_genes.fasta SeqSero/database/FljB_Family_k,z_special_genes.fasta SeqSero/database/FljB_Family_l,v_special_genes.fasta SeqSero/database/FljB_Family_l,w_special_genes.fasta SeqSero/database/FljB_Family_z_special_genes.fasta SeqSero/database/FljB_l,z13,z28_whole.fasta SeqSero/database/FljB_z6_whole.fasta SeqSero/database/H_combine_update_9_03_2014_new.fasta SeqSero/database/H_new_fliC_protein_database.fasta SeqSero/database/H_new_fljB_protein_database.fasta SeqSero/database/H_newest_database.fasta SeqSero/database/O_3,10_and_1,3,19_spe.fasta SeqSero/database/O_4_wzy_but_not_in_rfb.fasta SeqSero/database/ParaA_rfb.fasta SeqSero/database/ParaA_rfb.fasta.amb SeqSero/database/ParaA_rfb.fasta.ann SeqSero/database/ParaA_rfb.fasta.bwt SeqSero/database/ParaA_rfb.fasta.pac SeqSero/database/ParaA_rfb.fasta.sa SeqSero/database/Typhimurium_LT2_gnd_galF.fasta SeqSero/database/complete_oafA.fasta SeqSero/database/fliC_b_whole.fasta SeqSero/database/fliC_k,z_whole.fasta SeqSero/database/fliC_l_z13_whole.fasta SeqSero/database/fliC_r_whole.fasta SeqSero/database/fliC_r_whole.fasta.amb SeqSero/database/fliC_r_whole.fasta.ann SeqSero/database/fliC_r_whole.fasta.bwt SeqSero/database/fliC_r_whole.fasta.pac SeqSero/database/fliC_r_whole.fasta.sa SeqSero/database/fliC_z36,z38_whole.fasta SeqSero/database/fliC_z4,z23_family.fasta SeqSero/database/fliC_z4z23_whole.fasta SeqSero/database/fliC_z58_k_special_sequences.fasta SeqSero/database/fljB_e,n,z15_whole.fasta SeqSero/database/new_Oserotype.fasta SeqSero/database/oafA_of_O4_O5.fasta SeqSero/database/special_O_genes.fasta SeqSero/database/special_new_O_genes.fasta SeqSero/database/specific_genes.fasta SeqSero/database/tyr_of_O2_O9.fasta SeqSero/libs/BWA_analysis_H_update_new_family_dependent.py SeqSero/libs/BWA_analysis_O_new_dependent.py SeqSero/libs/H_combination_output_analysis.py SeqSero/libs/Initial_Conditions.py SeqSero/libs/Initial_Conditions.pyc SeqSero/libs/Initial_functions.py SeqSero/libs/Initial_functions.pyc SeqSero/libs/Otype_determine_analysis.py SeqSero/libs/compare_and_change_two_fastq_id.py SeqSero/libs/deletion_compare.py SeqSero/libs/isPcr SeqSero/libs/run_auto_All_for_assemblies.py SeqSero/libs/run_auto_All_for_web_multi_revise.py SeqSero/libs/special_gene_test_assemblies.py SeqSero/libs/splitPairedEndReads.pl SeqSero/libs/split_interleaved_fastq.pl SeqSero/primers/seq_primer_fliC.txt SeqSero/primers/seq_primer_fljB.txt SeqSero/seqsero.xml |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/LICENSE Wed Dec 06 15:59:29 2017 -0500 |
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| b'@@ -0,0 +1,339 @@\n+GNU GENERAL PUBLIC LICENSE\n+ Version 2, June 1991\n+ \n+ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>\n+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n+ Everyone is permitted to copy and distribute verbatim copies\n+ of this license document, but changing it is not allowed.\n+\n+ Preamble\n+\n+ The licenses for most software are designed to take away your\n+freedom to share and change it. By contrast, the GNU General Public\n+License is intended to guarantee your freedom to share and change free\n+software--to make sure the software is free for all its users. This\n+General Public License applies to most of the Free Software\n+Foundation\'s software and to any other program whose authors commit to\n+using it. (Some other Free Software Foundation software is covered by\n+the GNU Lesser General Public License instead.) You can apply it to\n+your programs, too.\n+\n+ When we speak of free software, we are referring to freedom, not\n+price. Our General Public Licenses are designed to make sure that you\n+have the freedom to distribute copies of free software (and charge for\n+this service if you wish), that you receive source code or can get it\n+if you want it, that you can change the software or use pieces of it\n+in new free programs; and that you know you can do these things.\n+\n+ To protect your rights, we need to make restrictions that forbid\n+anyone to deny you these rights or to ask you to surrender the rights.\n+These restrictions translate to certain responsibilities for you if you\n+distribute copies of the software, or if you modify it.\n+\n+ For example, if you distribute copies of such a program, whether\n+gratis or for a fee, you must give the recipients all the rights that\n+you have. You must make sure that they, too, receive or can get the\n+source code. 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To prevent this, we have made it clear that any\n+patent must be licensed for everyone\'s free use or not licensed at all.\n+\n+ The precise terms and conditions for copying, distribution and\n+modification follow.\n+\n+ GNU GENERAL PUBLIC LICENSE\n+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\n+\n+ 0. This License applies to any program or other work which contains\n+a notice placed by the copyright holder saying it may be distributed\n+under the terms of this General Public License. The "Program", below,\n+refers to any such program or work, and a "work based on the Program"\n+means either the Program or any derivative work under copyright law:\n+that is to say, a work containing the Program or a portion of it,\n+either verbatim or with modifications and/or translated into another\n+language. (Hereinafter, translation is included without limitation in\n+the term "modification".) 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Of course, the commands you use may\n+be called something other than `show w\' and `show c\'; they could even be\n+mouse-clicks or menu items--whatever suits your program.\n+\n+You should also get your employer (if you work as a programmer) or your\n+school, if any, to sign a "copyright disclaimer" for the program, if\n+necessary. Here is a sample; alter the names:\n+\n+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program\n+ `Gnomovision\' (which makes passes at compilers) written by James Hacker.\n+\n+ {signature of Ty Coon}, 1 April 1989\n+ Ty Coon, President of Vice\n+\n+This General Public License does not permit incorporating your program into\n+proprietary programs. If your program is a subroutine library, you may\n+consider it more useful to permit linking proprietary applications with the\n+library. If this is what you want to do, use the GNU Lesser General\n+Public License instead of this License.\n' |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/README.md Wed Dec 06 15:59:29 2017 -0500 |
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| @@ -0,0 +1,38 @@ +# SeqSero 1.0 +Salmonella serotyping from genome sequencing data + + +# Introduction +SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. A web app is available at www.denglab.info/SeqSero + +# Dependencies +SeqSero depends on: + +1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download); + +2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/); + +3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/); + +4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + +5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + +6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent. + +# Executing the code + Usage: SeqSero.py + + -m <int> (input data type, '1' for interleaved paired-end reads , '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly) + + -i <file> (/path/to/input/file) + + -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional) + +# Output +Upon executing the command, a directory named 'SeqSero_result_<time_you_run_SeqSero>' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory + +# Citation +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/SeqSero.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/SeqSero.py Wed Dec 06 15:59:29 2017 -0500 |
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| @@ -0,0 +1,60 @@ +#!/usr/bin/env python + +############################################################################ +# Copyright (c) 2014-2015 University of Georgia +# All Rights Reserved +############################################################################ + +import argparse,os,sys,time,random + +def main(): + parser = argparse.ArgumentParser(usage='SeqSero.py -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com') + parser.add_argument("-m", choices=['1','2','3', '4'],help="<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)") + parser.add_argument("-i", nargs="+", help="<string>: path/to/input_data") + parser.add_argument("-b",choices=['sam','mem','nanopore'],default="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam") + args=parser.parse_args() + dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + if len(sys.argv)==1: + os.system(dirpath+"/SeqSero.py -h") + else: + request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) + request_id += str(random.randint(1, 10000000)) + make_dir="SeqSero_result_"+request_id + os.system("mkdir "+make_dir) + os.system("cp -rf "+dirpath+"/database "+make_dir) + mode_choice=args.m + mapping_mode=args.b + dataset=args.i + if mode_choice=="1": + print dataset[0] + os.system("cp "+dataset[0]+" "+make_dir) + os.chdir(make_dir) + os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1") + print "\n\n\nResult:\n" + os.system("cat Seqsero_result.txt") + os.system("rm "+dataset[0].split("/")[-1]) + elif mode_choice=="2": + os.system("cp "+dataset[0]+" "+make_dir) + os.system("cp "+dataset[1]+" "+make_dir) + fnameA=dataset[0].split("/")[-1] + fnameB=dataset[1].split("/")[-1] + os.chdir(make_dir) + print "check fastq id and make them in accordance with each other...please wait..." + os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2") + print "\n\n\nResult:\n" + os.system("cat Seqsero_result.txt") + elif mode_choice=="3": + os.system("cp "+dataset[0]+" "+make_dir) + os.chdir(make_dir) + os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3") + print "\n\n\nResult:\n" + os.system("cat Seqsero_result.txt") + elif mode_choice=="4": + os.system("cp "+dataset[0]+" "+make_dir) + os.chdir(make_dir) + os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) + print "\n\n\nResult:\n" + os.system("cat Seqsero_result.txt") + +if __name__ == '__main__': + main() |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_b,d,j_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_b,d,j_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
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| b'@@ -0,0 +1,72 @@\n+>fliC_b_ParatyphiBstr_AOXH01000168\n+GATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGATGGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTACAGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTAAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGACCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCTGTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACC\n+>fliC_b_Salmonella.enterica_Paratyphi.B_AY353359\n+GATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGATGGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTACAGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTAAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGACCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCTGTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACT\n+>fliC_b_Salmonella.enterica_Paratyphi.B_AY353358\n+GATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGATGGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTACAGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTAAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGACCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCTGTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACT\n+>fliC_b_Salmonella.enterica_I.6,7:b:z33_AY353361\n+GATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGATGGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTACAGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTAAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGACCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCTGTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACC\n+>fliC_b_Salmonella.enterica_Niederoderwitz_AY353360\n+GATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTGACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGATGGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTACAGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTG'..b'CTAGCACAGTTACCGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTTAATTATACTGACGCTACTGGTGCAGCAAAAACTGGTGCTGTGAAATTTGGTGGTGCGAATGGTAAGACTGAAGTTGTGACCACAGTTGATGGTAATACTTATCAAGCTAGTGATGTTAAAGGACATAATTTCCAGAGTGGCGGCGCTTTAAGCGAGGCTGTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGGTGCGGTACAGAACCGT\n+>fliC_d_Schwarzengrundstr_ABEJ01000027\n+GATTTAAAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAAAAATGGTACAGATACTGTTACAGCCCAGAGCAATACTGATATCGAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGG\n+>fliC_d_Salmonella.enterica_Schwarzengrund_AY353371\n+GATTTAAAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAAAAATGGTACAGATACTGTTACAGCCCAGAGCAATACTGATATCGAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCGTTCTGACC\n+>fliC_d_Muenchenstr_ARYW01000085\n+GATATTGATTTAAAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAATAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGT\n+>fliC_d_Muenchenstr_ARYX01000110\n+GATTTAAAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTT\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_fg_special.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_fg_special.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,9 @@ +>fliC_f,g_Salmonella.enterica_Derby_AY353380 +AATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGAC +>fliC_f,g,s_Salmonella.enterica_Agona_AY353383 +GATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAGAACAACACTGCGGTTAAC +>fliC_f,g,t_Salmonella.enterica_Berta_AY353532 +GATAAAGTATACGTAAACGCTGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGAC +>fliC_f,g,t_Salmonella.enterica_II.17:f,g,t:e,n,x,z15_AY353534 +GATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGAT + |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_g_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_g_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,452 @@\n+>fliC_g,m_Enteritidisstr_ALGY01000052_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGX01000033_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_AHUL01000064_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALFE01000865_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGR01000023_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_AHUN01000143_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_AHUR01000042_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_CAGR02000072_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGS01000033_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGW01000034_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGACGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGU01000066_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTAC\r\n+>fliC_g,m_Enteritidisstr_ALGZ01000018_g,m\r\n+ATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCT'..b'TAAATCTACTAAATCTGCTGCAGGTACTGACGATGCCAAGGCTATCGCAACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTGATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGCGAGTGCAACAGACGT\r\n+>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353410_g,m\r\n+ACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCCGATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGCAACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTGATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGTGGGTGCAGCAGACGTAAATAGCGCGAAGATT\r\n+>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353409_g,m\r\n+ACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCCGATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGCAACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTGATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTAGCGTGGGTGCAGCAGACGTAAATAGCGCGAAGATT\r\n+>fliC_g,m,t_Salmonella.enterica_II.6,8:g,m,t:1,7_AY353537_g,m\r\n+ATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAAAATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCATTAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAGCTGGTAATGATGGTAATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCGGTGGTGGTAGTGTTAATGATGCTACCTTACAATCAAGCAGA\r\n+>fliC_g,m,t_Salmonella.enterica_II.28:g,m,t:e,n,x_AY353536_g,m\r\n+ATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAAAATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCATTAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAAATGGTAATGATGGTAATGGTACTGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGGTGGTGGTAGTGTTAATGATGCTACCTTACAATCAAGCAGA\r\n+>fliC_f,g,m,t_Salmonella.enterica_II.6,8:f,g,m,t:.e,n,x_AY353382_g,m\r\n+ATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAAAATAACACTGCAGTTGCTCTATTCAATACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCATTAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTAATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTTAATGATGC\r\n+>fliC_f,g,t_Salmonella.enterica_Berta_AY353533_g,m\r\n+ACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCAATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCGAATGT\r\n+>fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m\r\n+ACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCAATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCGAATGTTGA\r\n+>fliC_g,z51_Salmonella.enterica_Travis_AY353413_g,m\r\n+GGTACCGATAAGATTTACGTAAATGCAGCAAACGGTCAGCTCACAACTGATGATGCACAGAATAACACTGCAGTTGATCTATTTAAGACAGCAAAATCATCAGCAGGTACAGCTGAATCTAAAGCAATAGCTGGCGCTATTAAAGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTCACCATTGATACAAAGAATGGCGCTGACGGTAATGGTACTGTTTCCACTATGATCAATGGTGAAAAAGTTACGTTGACTGTTGCTGATATTACCACTGGTGCGGCGGACGTTAATGCGGCTAC\r\n+>fliC_g,z51_50_g,z51_-str_AOXJ01000042_g,m\r\n+GGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAATAACACCCCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAAAGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATGGTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAATGCGGCAAC\r\n+>fliC_g,z51_Salmonella.enterica_IIIa.45:g,z51:-_AY353414_g,m\r\n+GGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAATAACACCGCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAAAGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATGGTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAATGCGGCAAC\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_k,z_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_k,z_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,52 @@\n+>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436\n+GATAGCAAACCAGCGCAGAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCCTAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAAGGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAACTAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAGCAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTT\n+>fliC_k_Salmonella.enterica_IIIb.61:k:1,5_AY353539\n+GATAGCAAACCAGCGCAGAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCCTAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAAGGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAACTAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAGCAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAA\n+>fliC_k_Salmonella.enterica_IIIb.50:k:z_AY353538\n+GATAGCAAACCAGCGCAGAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCCTAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATTCTGCTAAAAGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAACTAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAGCAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAA\n+>fliC_k_Salmonella.enterica_IIIb.50:k:z53_AY353440\n+GATAGCAAACCAGCGCAGAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCCTAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAAGGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAACTAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAGCAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAA\n+>fliC_k_Salmonella.enterica_IIIb.17:k:z_AY353437\n+GATAGCAAACCAGCGCAGAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCCTAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAAGGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAACTAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAGCAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTT\n+>fliC_(k)_Salmonella.enterica_IIIb.16:(k):e,n,x,z15_AY353541\n+GATAGCAAACCAACAAGTATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTAAAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGCGGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAAACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAGGCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATG\n+>fliC_k_Salmonella.enterica_IIIb.65:(k):z_AY353438\n+GATAGCAAACCAACAAGTATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTAAAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGCGGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAAACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAGGCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATG\n+>fliC_(k)_Salmonella.enterica_IIIb.42:(k):z35_AY353542\n+GATAGCAAACCAACAAGTATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTAAAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGCGGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAAACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAGGCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTC\n+>fliC_k_Salmonella.enterica_IIIb.38:(k):z53_AY353540\n+GATAGCAAACCAACAAGTATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTAAAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGCGGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAAACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAGGCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTC\n+>fliC_k_Salmonella.enterica_IIIb.38:(k):z35_AY353439\n+GATAGCAAACCAACAAGTATGAAGTTGGATACTAGC'..b'TTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGCGTCGATGCTGCTGATGCAGCTACG\n+>fliC_z41_Salmonella.enterica_Maska_AY353511\n+GATAGCAAAGCTGTTACTGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGTATCAGTGCAGGTAATCCTGCTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACGAAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTACTCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGATGGCTGGAAATATTGATACTGCTGATGCAGATGCTGCTGAAATGGTCAAAATG\n+>fliC_z_Salmonella.enterica_II.40:z:z42_AY353470\n+GATAGCAAAGCTGTGACCGGTGTTTCTACTTTGGATACTGCAGGACTTACTGGCGCAGCTATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTGGTTCCATTAAAGATGGCAAAGTATACTTTGATGATGCTACTAAAAATTATTATGTTGAAGTAGAGTTTTCTGATGCCGCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGTACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCCGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGTTGATGTGAAAGCTGCTCTGACTGCTGGTGGCGTTGATACTGCTGATGCAGCTACGGCAGAAATG\n+>fliC_k_Invernessstr_AOZD01000019\n+CAAGCTACAGTTGAAAACAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCCTCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAAAATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGCAAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAGCTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCT\n+>fliC_k_Salmonella.enterica_Inverness_AY353441\n+CAAGCTACAGTTGAAAACAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCCTCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAAAATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGCAAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAGCTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTG\n+>fliC_z44_Salmonella.enterica_Quinhon_AY353513_k,z\n+GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTGACTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTGCTAAAAATTATTATGTTGAAGTAGACTTTTCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGACGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGTGTCGATACTGCTGATGTAGCTACGGCAGAAATG\n+>fliC_z_Salmonella.enterica_Poona_AY353467\n+GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTGGCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGTGTCGATGCTGCTGATGTAGCTACG\n+>fliC_z41_Salmonella.enterica_Ottawa_AY353510\n+GATAGCAAAGCTGTTACTGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGGATCAGTGCAGGTAATCCTGCTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACGAAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTACTCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGATTGCTGGAGATATTGATACTGCTGATGCAGATGCTGCTGAAATG\n+>fliC_z44_Salmonella.enterica_Bulovka_AY353512_k,z\n+CAAGCTACAGTTGAAAACAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCCTCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGGCTGACTCAGGTAAAAATGGTTTCCTTAAAGTTGATGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAAATACTGTAGCAGCAAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCAAGTTCGGCTGTACAAGATCAGTTAACAGCTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAA\n+>fliC_z69_Salmonella.enterica_Pietersburg_AY353520\n+GATAGTAAAGCTGTAACAGTAGCTGCTGATTTAGATATTACCGCTCTTAATACCGATGCAGCTCTTAAAGCAGGAACGGGAGCTACAACAGGTACTCCATCAATAAAAGATGACAAAGTTTATTATGATAGTGCCAGCAAAAACTACTACGTTGAAGTTACCGGATTAACCGCCCCTGATGATGCTAAGAATGGCTTCTATAAAGTAAATGTTGCTGATGACGGTACAGTATCCATGGCCGCTAATACAGCTATAGAGGCGGGTAAACCAGCCGGTGCAGTAGAAGTAACAAAAACTCAAGAAGAAAAAAACCCATTACCATTATCAGCAGATCTCAAAACTTCTCTTAAATCTGGCGAGATTACAGATCCAGACATT\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_k_z58_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_k_z58_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>fliC_z58_Salmonella.enterica_I.47:z58:-_AY353518 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTTTGGACTCACTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_Blockley_AY353442 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Invernessstr_AOZD01000019 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_Inverness_AY353441 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Thompsonstr_AOXP01000022 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Thompsonstr_AMSN01000007 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTAT +>fliC_k_Salmonella.enterica_IIIb.61:k:1,5_AY353539 +ATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTAT +>fliC_k_Salmonella.enterica_IIIb.50:k:z_AY353538 +ATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTAT +>fliC_(k)_Salmonella.enterica_IIIb.16:(k):e,n,x,z15_AY353541 +TCGATCTGAAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.65:(k):z_AY353438 +TCGATCTGAAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.50:k:z53_AY353440 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTAT +>fliC_(k)_Salmonella.enterica_IIIb.42:(k):z35_AY353542 +TCGATCTGAAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.38:(k):z53_AY353540 +TCGATCTGAAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.38:(k):z35_AY353439 +TCGATCTGAAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTAT +>fliC_k_Salmonella.enterica_IIIb.17:k:z_AY353437 +TCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTAT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_l,v_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_l,v_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,24 @@ +>fliC_l,v_Salmonella.enterica_Brandenburg_AY353444 +AATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACG +>fliC_l,v_Salmonella.enterica_Give_AY353443 +AATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACG +>fliC_l,z13_Salmonella.enterica_Westerstede_AY353450 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG +>fliC_l,z13_Salmonella.enterica_Kenya_AY353449 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTCATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACTACG +>fliC_l,w_Salmonella.enterica_Glidji_AY353447 +AATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG +>fliC_l,z28_Salmonella.enterica_Javiana_AY353455 +AGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCC +>fliC_l,z28_Salmonella.enterica_Javiana_AY353454 +AGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCC +>fliC_l,z13,z28_Salmonella.enterica_Fallowfield_AY353453 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCC +>fliC_l,z13,z28_Salmonella.enterica_Connecticut_AY353452 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCCGCG +>fliC_l,w_Salmonella.enterica_Ayton_AY353446 +AATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACTAAA +>fliC_l,v_Litchfieldstr_APAN01000015 +AATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAAA +>fliC_l,v_Salmonella.enterica_IIIb.38:l,v:z54_AY353445 +AGTACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACTGCTGCCATTAAAGATAATAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTGCTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCACG |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_r,i_special_genes_short.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_r,i_special_genes_short.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,46 @@\n+>fliC_r_Heidelbergstr_ABEL01000019\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMLT01000023\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMBX01000033\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMBW01000024\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMBV01000021\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMBU01000009\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_r_Heidelbergstr_AMMX01000026\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACT\n+>fliC_r_Heidelbergstr_AJGW01000023\n+CTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAAT\n+>fliC_r_Infantisstr_ATHK01000035\n+CTGTCACTGGCTATACAGATT'..b'_AFYI01000002\n+CTGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAAT\n+>fliC_i_Salmonella.enterica_Augustenborg_AY353426\n+CTGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTGACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACT\n+>fliC_i_Salmonella.enterica_Idikan_AY353422\n+CTGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTGACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACT\n+>fliC_i_Salmonella.enterica_Augustenborg_AY353418\n+CTGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTGACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACT\n+>fliC_r,i_Salmonella.enterica_Bovismorbificans_AY353463\n+CTGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGAT\n+>fliC_i_Salmonella.enterica_II.4,12,27:i:z35_AY353425\n+CTGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAGACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAAT\n+>fliC_i_Salmonella.enterica_IIIb.48:i:z_AY353419\n+CTGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAGACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAAT\n+>fliC_i_Salmonella.enterica_IIIb.61:i:z_AY353417\n+CTGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAGACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCCTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAAT\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_z36z38_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_z36z38_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>fliC_z36,z38_Salmonella.enterica_IV.43:z36,z38:-_AY353486 +GCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAGAATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +>fliC_z36_Salmonella.enterica_Potosi_AY353482 +GCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGCGCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAGAATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT +>fliC_z38_Salmonella.enterica_Lille_AY353488 +GCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACGGGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTACGAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAGAATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +>fliC_z38_Salmonella.enterica_Fresno_AY353487 +GCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACGGGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTACGAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAGAATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +>fliC_z36,z38_Salmonella.enterica_IV.1,53:z36,z38:-_AY353485 +GCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAGAATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +>fliC_z36_Salmonella.enterica_IIIa.43:z36:-_AY353484 +GCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGCGCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAACTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACAAAAGGAATTGCTACAACGGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAGAATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATACAGCAAACAGTAAATATTACGACGCAACTGTAGATGCT +>fliC_z36_Salmonella.enterica_Weslaco_AY353483 +GCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGCGCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAGAATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_z44_k_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_z44_k_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>fliC_(k)_Salmonella.enterica_IIIb.42:(k):z35_AY353542 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_(k)_Salmonella.enterica_IIIb.16:(k):e,n,x,z15_AY353541 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.38:(k):z53_AY353540 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.61:k:1,5_AY353539 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.50:k:z_AY353538 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.38:(k):z35_AY353439 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.65:(k):z_AY353438 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.50:k:z53_AY353440 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_IIIb.17:k:z_AY353437 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Salmonella.enterica_Blockley_AY353442 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Thompsonstr_AOXP01000022 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Thompsonstr_AMSN01000007 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAG +>fliC_k_Invernessstr_AOZD01000019 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAG +>fliC_k_Salmonella.enterica_Inverness_AY353441 +AGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAG +>fliC_z44_Salmonella.enterica_Bulovka_AY353512 +AGGCAATTGCTAACCGTTTTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACTAACTCCCAG |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_Family_z4z23_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_Family_z4z23_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,90 @@\n+>fliC_z4,z23_Salmonella.enterica_IV.1,40:z4,z23:-_AY353492\r\n+ATAACGCAAAAGCAACTGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Salmonella.enterica_IV.38:z4,z23:-_AY353499\r\n+ATAACGCAAAAGCAACGGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Salmonella.enterica_IIIa.43:z4,z23:-_AY353495\r\n+ATAACGCAAAAGCAACGGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUR01000024\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUS01000023\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUT01000021\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUU01000023\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUV01000029\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Cerrostr_AYUW01000021\r\n+ATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGA'..b'erica_IIIa.44:z4,z23,z32:-_AY353502\r\n+AAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTATCTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTT\r\n+>fliC_z4,z23_Salmonella.enterica_IIIa.62:z4,z23:-_AY353545\r\n+ATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACC\r\n+>fliC_z4,z23_Salmonella.enterica_IIIa.40:z4,z23:-_AY353496\r\n+ATAACGCAAAAGCAACTGGTGGTCCTGCTGCGGATAAATTATCTCTGACAAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACT\r\n+>fliC_z4,z23_Salmonella.enterica_IIIa.41:z4,z23:-_AY353547\r\n+ATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCATTC\r\n+>fliC_z4,z23_Salmonella.enterica_IIIa.18:z4,z23:-_AY353546\r\n+ATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAA\r\n+>fliC_z4,z24_Salmonella.enterica_IIIa.53:z4,z24:-_AY353505\r\n+AAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAATTATCTTTGGTAAAAGATGATAAAGGAAACTATCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCTACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTCACTTTAGCTGGTGGTGCTTCAACCCCAAGTGCGGTTGATACTTTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGAT\r\n+>fliC_z4,z32_Salmonella.enterica_IIIa.63:z4,z32:-_AY353508\r\n+AAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTATCTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAA\r\n+>fliC_z4,z32_Salmonella.enterica_IIIa.18:z4,z32:-_AY353543\r\n+AAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTATCTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAA\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FliC_f_g_s_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FliC_f_g_s_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,15 @@\n+>fliC_f,g,s_Salmonella.enterica_Agona_AY353383\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTGCTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAGAACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTTGATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_g,m_Salmonella.enterica_Enteritidis_AY353388\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTGCTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_f,g_Salmonella.enterica_Derby_AY353381\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCTACAGTGGGTGATCTGAAGTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTGCTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAG'..b'AGCTCACAACTGATGATGCACAGAATAACACTGCAGTTGATCTATTTAAGACAGCAAAATCATCAGCAGGTACAGCTGAATCTAAAGCAATAGCTGGCGCTATTAAAGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTCACCATTGATACAAAGAATGGCGCTGACGGTAATGGTACTGTTTCCACTATGATCAATGGTGAAAAAGTTACGTTGACTGTTGCTGATATTACCACTGGTGCGGCGGACGTTAATGCGGCTACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTAAACGGCCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGCGCTGAGTATACAGCTAACGCTGAAGGTGATAAAGTTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACCGCTTCTGGCGTTAGCACATTAATCAATGAAGATGCTGCTGCTGCTAAGAAGAGTACAGCTAATCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGATGCTGTACGTTCTTCACTGGGGGCGATCCAGAATCGCTTTGATTCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_f,g,t_Salmonella.enterica_II.17:f,g,t:e,n,x,z15_AY353534\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTCCGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACGGCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTGCTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTTAATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_m,t_Salmonella.enterica_Oranienburg_AY353411_g,m\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGGCGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCCGATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGCTGCAGGTACTGACGATGCCAAGGCTATCGCAACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTGATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGCGAGTGCAACAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCCAAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_1_2_7_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,12 @@\n+>fljB_1,5_Salmonella.enterica_IIIb.61:k:1,5_AY353278\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAACAACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGACTGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTGTATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA\r\n+>fljB_1,7_Salmonella.enterica_Bredeney_AY353296\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACAACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGCTGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTGTTTCCGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA\r\n+>fljB_1,2_Salmonella.enterica_Typhimurium_AY353264\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACAACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTA'..b'ACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTACGGGGGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTGTTTCAACAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTGGACGCTACCAATGCTAATGGCGCCGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA\r\n+>fljB_1,5,7_Salmonella.enterica_IIIb.48:l,w:1,5,7:z50_AY353274\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAACAACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGACTGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTGTATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA\r\n+>fljB_1,6_Salmonella.enterica_Agama_AY353294\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACCACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTGGTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGTGGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCCTGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTGTTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_1_2_7_whole.fasta.amb Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +9126 6 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_1_2_7_whole.fasta.ann Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,13 @@ +9126 6 11 +0 fljB_1,5_Salmonella.enterica_IIIb.61:k:1,5_AY353278 (null) +0 1521 0 +0 fljB_1,7_Salmonella.enterica_Bredeney_AY353296 (null) +1521 1521 0 +0 fljB_1,2_Salmonella.enterica_Typhimurium_AY353264 (null) +3042 1521 0 +0 fljB_1,2,7_Salmonella.enterica_Kambole_AY353275 (null) +4563 1521 0 +0 fljB_1,5,7_Salmonella.enterica_IIIb.48:l,w:1,5,7:z50_AY353274 (null) +6084 1521 0 +0 fljB_1,6_Salmonella.enterica_Agama_AY353294 (null) +7605 1521 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta.bwt |
| b |
| Binary file SeqSero/database/FljB_1_2_7_whole.fasta.bwt has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta.pac |
| b |
| Binary file SeqSero/database/FljB_1_2_7_whole.fasta.pac has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_1_2_7_whole.fasta.sa |
| b |
| Binary file SeqSero/database/FljB_1_2_7_whole.fasta.sa has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_1_special_genes_all.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_1_special_genes_all.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,238 @@\n+>fljB_1,2_Typhimuriumstr_AERV01000016\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AMEA02000051\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AMDZ02000041\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_ATWR01000017\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AMEE02000100\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AOXD01000102\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AJTU01000003\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AOXO01000107\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AHUZ01000007\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AHVA01000007\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQL01000023\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQN01000019\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQO01000019\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQM01000018\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AHUV01000080\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AOXC01000008\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQV01000001\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2_Typhimuriumstr_AUQU01000007\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGA'..b'CCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATCTCGACAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_Bovismorbificans_AY353283\r\n+AGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTGGTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGGGGCTTTAGTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2,7_Salmonella.enterica_Kambole_AY353277\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2,7_Salmonella.enterica_Eingedi_AY353276\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,2,7_Salmonella.enterica_Kambole_AY353275\r\n+GCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_I.43:e,h:1,5_AY353284\r\n+ACTTATGCCGATAATGGTATTACACTGGATGCCTCAGGCCTTGATGATGCAGCCATCAAAGCGGCCATTGGTGGTACGACTGGTACGGCTGCTGTTACGGGTGGTACAGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGGGGCTTTAGTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,5_Infantisstr_AFYI01000002\r\n+AGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTGGTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGGGGCTTTAGTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,5,7_Salmonella.enterica_Hisingen_AY353289\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATTAAAGCAGCTACGGGGGGGACGGCTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGTTGCCAAAAATGGC\r\n+>fljB_1,5,7_Salmonella.enterica_IIIb.47:r:1,5,7_AY353291\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5,7_Salmonella.enterica_IIIb.48:l,v:1,5,(7)_AY353290\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5,7_Salmonella.enterica_IIIb.48:l,w:1,5,7:z50_AY353274\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5,7_Salmonella.enterica_IIIb.6,7:l,v:1,5,7_AY353273\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_61:l,v:1,5_AY353279\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_IIIb.61:k:1,5_AY353278\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_Rough:r:1,5_AY353281\r\n+GCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTGGTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGGTGATGCTGCCAAAAATGGC\r\n+>fljB_1,5_Choleraesuis_var._Kunzendorf_BCW_6194(CDC)\r\n+AGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATACAGCTATCAAAGCGGCTATAGGTGGTACGACTGGTACGGCTGCTGTAACCGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGC\r\n+>fljB_1,5_Salmonella.enterica_Muenster_DTU-unknown\r\n+ACTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTGGTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGTGGCTATACTGGTGCTGATGCATCCAAAAATGGC\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_e_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_e_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,60 @@ +>fljB_e,n,x_Salmonella.enterica_Singapore_AY353305 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,z15_Salmonella.enterica_Uno_AY353325 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCTAAAAATGGC +>fljB_e,n,x_Salmonella.enterica_Kokomlemle_AY353319 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCGGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,z15_Braenderupstr_AOZM01000055 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC +>fljB_e,n,z15_Salmonella.enterica_Braenderup_AY353324 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC +>fljB_e,n,x_Salmonella.enterica_Bessi_AY353317 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Bonn_AY353308 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,z15_Salmonella.enterica_Brandenburg_AY353323 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC +>fljB_e,n,z15_Mbandakastr_AMRS01000032 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC +>fljB_e,n,x_Rubislawstr_AOYA01000090 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Minnesotastr_AOYO01000082 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Tambacounda_AY353318 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,z15_Salmonella.enterica_Sanktgeorg_AY353326 +AGGCGCTTACAGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCTACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC +>fljB_e,n,x_Chesterstr_AOZI01000020 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Chester_AY353321 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCAGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Chester_AY353307 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Hadarstr_ABFG01000005 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Hadarstr_AOZE01000017 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Hadarstr_ARYR01000012 +AGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Gatuni_AY353322 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_Tiergarten_AY353315 +AGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGACGGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACTGCCAAGAATGGT +>fljB_e,n,x_Salmonella.enterica_II.9,46:e,n,x:1,5,7_AY353316 +AGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACAGCCAAAAATGGT +>fljB_e,n,x_Salmonella.enterica_II.56:e,n,x:1,7_AY353314 +AGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACAGCCAAAAATGGT +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353309 +AGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGACGGTAACTGGTGATACATTAACTGCCACCGTATCCTTTAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGATGCGGGGGATGTTGCCAAAAATGGC +>fljB_e,n,x,z15_Salmonella.enterica_16:z10:e,n,x,z15_AY353306 +AGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGACGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGATACGGGGGATGCTGCCAAAAATGGC +>fljB_e,n,x_Salmonella.enterica_II.9,12:lw:enx_AY353320 +AGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGATGCGGGGGATACAGCCAAAAATGGT +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.57:i:e,n,x,z15_AY353312 +AGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGACGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGATACGGGGGATGCTGCCAAAAATGGC +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.47:i:e,n,x,z15_AY353313 +AGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGACGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGATACGGGGGATGCTGCCAAAAATGGC +>fljB_e,n,x,z15_Salmonella.enterica_Verity_AY353311 +AAGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACCGTAGGTGGTTATACCGATACGGGGGATGCTGCCAAAAATGGC +>fljB_e,n,z15_Salmonella.enterica_Sandiego.var.d+_AY353303 +AGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGC |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_k,z_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_k,z_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,36 @@ +>fljB_z_Salmonella.enterica_IIIb.53:z:1,5,(7)_AY353338 +GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.48:z:1,5,(7)_AY353339 +GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.48:i:z_AY353336 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.61:i:z_AY353335 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z6_Kentuckystr_AOYY01000105 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Weltevredenstr_ABFF01000037 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Sloterdijkstr_AOXT01000012 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQI01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_ABAK02000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AOYZ01000091 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AHUU01000123 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQH01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQJ01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQF01000002 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AYDR01000034 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Salmonella.enterica_Weltevreden_AY353353 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Salmonella.enterica_Bere_AY353352 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_l,v_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_l,v_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>fljB_l,w_Salmonella.enterica_Ohio_AY353331 +AATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG +>fljB_l,z13,z28_Salmonella.enterica_Lutetia_AY353334 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGCG +>fljB_l,w_Salmonella.enterica_Gloucester_AY353332 +CTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAAA +>fljB_l,z13,z28_Salmonella.enterica_Poano_AY353333 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_l,w_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_l,w_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>fljB_l,w_Salmonella.enterica_Ohio_AY353331 +AATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACG +>fljB_l,z13,z28_Salmonella.enterica_Lutetia_AY353334 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGCG +>fljB_l,w_Salmonella.enterica_Gloucester_AY353332 +CTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACGGTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAAA +>fljB_l,z13,z28_Salmonella.enterica_Poano_AY353333 +AGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_Family_z_special_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_Family_z_special_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,36 @@ +>fljB_z_Salmonella.enterica_IIIb.53:z:1,5,(7)_AY353338 +GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.48:z:1,5,(7)_AY353339 +GATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.48:i:z_AY353336 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z_Salmonella.enterica_IIIb.61:i:z_AY353335 +GATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATG +>fljB_z6_Kentuckystr_AOYY01000105 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Weltevredenstr_ABFF01000037 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Sloterdijkstr_AOXT01000012 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQI01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_ABAK02000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AOYZ01000091 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AHUU01000123 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQH01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQJ01000001 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AUQF01000002 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Kentuckystr_AYDR01000034 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Salmonella.enterica_Weltevreden_AY353353 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT +>fljB_z6_Salmonella.enterica_Bere_AY353352 +GATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_l,z13,z28_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_l,z13,z28_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fljB_l,z13,z28_Salmonella.enterica_Lutetia_AY353334 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTGAAACAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAAAAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGCGAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z39_Salmonella.enterica_II.4,12:g,m,t:z39_AY353346 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTACAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTGAAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGACTGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAACTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTATACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAAAATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGATGTTAAAACACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAATGGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTTTAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTAAAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGATCTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGTTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAGCACGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/FljB_z6_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/FljB_z6_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fljB_z6_Salmonella.enterica_Weltevreden_AY353353 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTTTTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAAAATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTGGTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCTGATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGAAGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAGCTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAACGGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/H_combine_update_9_03_2014_new.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/H_combine_update_9_03_2014_new.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,1385 @@\n+>fliC_z65_Salmonella.bongori_V.66:z65:-_AY353259_other.z65\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCACTGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTTTTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCACTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACGGCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTGAAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAGGATGAAGCTGTTACTGCTGGTACTTTCAGTGTAGATAGTGGTGTGGCAATTAAATCTGCAACGGTTGACGTTAAAACAGCTTTAAGCACGACTGGTAATGACGGTACTGTAAGTAAAATTGAACTTGATAAGGCAACAGGTAAATATTACGCAACTGTATCAGGGCTTACAGATTCTGCAGATACAAGTAAAAATGGCACTTATGAAGTTAATGTTAGTTCTACTGGCGATATTACTTTTGTTGATACAACCAAAGACACTGTCACTGCTGGCTCGGTAGAAGTACAAAATGTTCATACGAAAGCTGCTGGTGCACTTCCTGATTTAGCCGACGCAAAAGCAGCTTTAACCAAAGCCAATGTTGCTAATGCAGACACTGCTTCTTTAGTGAAAATGTCTTATACGGATAAGAACGGTAAGGTCATTGACGGCGGTTATGCATTAAAAACAGATGATACCAAATATTATGTTGCATCATATAACGAAACTACTGGAAAAGTCGAAGCTGCGGTTACAAAATATACCGATTCAAATGGATTTTCTAAAACAGCTGCTAATCAATTAGGTGGTGTAGATCGCAAAACAGAAGTTGTGGAAATTGGTGGTAAAACTTACACAGCAGCCAAAGCTAAAGACCATAACTTTAAAGCTGATCCAGATCTGGCAGTTGTTGCAGCTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCACAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACCTCCGTTCTGGCACAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z81_Salmonella.bongori_66:z81:-_AY353260_other.z81\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCACTGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTTTTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACGGCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATCGATCTGAAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCACGCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTTCTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACAGCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAACGACAACCCCAACAGGTATTACTGCAGTGGCTCAGGTTCAGAAGCCTGTAGCAGCGCCATCAGCTATCCAGGATCAGTTGACAGCGGCAAGTGTTGCTAATGCTGACAAAGCAGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACTATTGATGGCGGTTACGCTGTAAAAGTGGGGGACGATTACTACGCTGCTACTCAGAAAAAAGACGGTAGCTTTACCATTAACACCACTTCTTACACGGATAAAGATGGTAATACGCAAACTGCACTCAATAAATTAGGCGGCGTTGACGGAAAAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCTAAAGCAAAAGATCATAATTTCAAAGCTGATCCTGATCTGGCGGAAGCGGCTACTACAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCAGGGACCTCCGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z81_Salmonella.bongori_40:z81:-_AY353261_other.z81\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCACTGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTTTTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCTGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATTGATCTGAAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCACGCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTTCTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACAGCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAACGAC'..b'ACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGCTGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTGTTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT\r\n+>fljB_z6_Weltevredenstr_ABFF01000037_k,z\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTTTTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAAAATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT\r\n+>fljB_z53_IIIb.60:(k):z53_HM142067_other.z53\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCG\r\n+CACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGG\r\n+TCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGAC\r\n+GGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTG\r\n+AACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATCAC\r\n+CCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAG\r\n+GATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTGAAGCAGATCA\r\n+ACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC\r\n+TGATGCTAAGACTATTGATCTCTCCGCCTTAAACGAAGCCGCGCTCAAAGCTGGTACTACTGGTACAACA\r\n+GGTGCTCCGGTCGTTAAAGATGATAAAATTTATTATGACGAAGCCAGTAAAAACTACTATGTTGAGGTTG\r\n+ATGGTTTCACTACTGGTGATGTAGGTAAAAACGGTTTTTATAAAGTTACTGTTGATGCTGATGGTAAAGC\r\n+GACTATGGCTGCCTCTACTACGATGGAGGCTGCGAAACCAGCTGGCGCTGTCGAAGTGACTAAGACTCAA\r\n+ACAGAAACACCAGTTAAACTAAGCGCAGCACTTAAAAAATCGTTGACTGATGGTGGTGTTGACACTGCTG\r\n+CTGCAGGTACTGCCCAAATTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGATGGCGGTTA\r\n+CGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACACC\r\n+ACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAA\r\n+CCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACA\r\n+GCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCA\r\n+CAGGTTGACACGTTACGTTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGG\r\n+GCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTC\r\n+CAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCA\r\n+CAAAACGTGCTGTCTCTGTTACGTTAA\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/H_new_fliC_protein_database.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/H_new_fliC_protein_database.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,946 @@\n+>z65__Salmonella.bongori__V.66:z65:-__AY353259__other.z65\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLSQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDEAVTAGTFSVDSGVAIKSATVDVKTALSTTGNDGTVSKIELDKATGKYYATVSGLTDSADTSKNGTYEVNVSSTGDITFVDTTKDTVTAGSVEVQNVHTKAAGALPDLADAKAALTKANVANADTASLVKMSYTDKNGKVIDGGYALKTDDTKYYVASYNETTGKVEAAVTKYTDSNGFSKTAANQLGGVDRKTEVVEIGGKTYTAAKAKDHNFKADPDLAVVAAATTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>z81__Salmonella.bongori__66:z81:-__AY353260__other.z81\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLSQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKKYDVKSEVATPTAKLDISGLDGAALKTGTGSTGDTGSIKDGKVYYDGTDYYAEITFTDTADQTAKGGYYKVNVDDATGAVTMTASTTKETTTPTGITAVAQVQKPVAAPSAIQDQLTAASVANADKAEMVKMSYTDKNGKTIDGGYAVKVGDDYYAATQKKDGSFTINTTSYTDKDGNTQTALNKLGGVDGKTEVVSIEGKTYTAAKAKDHNFKADPDLAEAATTTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>z81__Salmonella.bongori__40:z81:-__AY353261__other.z81\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLSQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKKYDVKSEVATPTAKLDISGLDGAALKTGTGSTGDTGSIKDGKVYYDGTDYYAEITFTDTADQTAKGGYYKVNVDDATGAVTMTASTTKETTTPTGITAVAQVQKPVAAPSAIQDQLTAASVANADKAEMVKMSYTDKNGKTIDGGYAVKVGDDYYAATQKKDGSFTINTTSYTDKDGNTQTALNKLGGVDGKTEVVSIEGKTYTAAKAKDHDFKAQPELAEAATATTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>a__Salmonella.enterica__Paratyphi.A__AY353356__other.a\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQKKYDVKSEAVTPSATLSTTALDGAGLKTGTGSTTDTGSIKDGKVYYNSTSKNYYVEVEFTDATDQTNKGGFYKVNVADDGAVTMTAATTKEATTPTGITEVTQVQKPVAAPAAIQAQLTAAHVTGADTAEMVKMSYTDKNGKTIDGGFGVKVGADIYAATKNKDGSFSINTTEYTDKDGNTKTALNQLGGADGKTEVVSIDGKTYNASKAAGHNFKAQPELAEAAAATTENPLAKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>a__Salmonella.enterica__Paratyphi.A__AY353357__other.a\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQKKYDVKSEAVTPSATLSTTALDGAGLKTGTGSTTDTGSIKDGKVYYNSTSKNYYVEVEFTDATDQTNKGGFYKVNVADDGAVTMTAATTKEPTTPTGITEVTQVQKPVAAPAAIQAQLTAAHVTGADTAEMVKMSYTDKNGKTIDGGFGVKVGADIYAATKNKDGSFSINTTEYTDKDGNTKTALNQLGGADGKTEVVSIDGKTYNASKAAGHNFKAQPELAEAAAATTENPLAKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>b__Salmonella.enterica__Paratyphi.B__AY353358__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLSVQDAYTPKGTAVTRDVTTYKNGGTTLTAPNAAAIDTALGTTGAAGTAAVKFKDGNYFVEVTGTTKDGLYEATVDAAGAVTMTANKATVTGASTVTENQIVDAVTPTPVDTVAAATALTNAGVTGATGNTSLVKMSFEDKNGKVTDAGYALKVGNDYYAADYDEKTGEIKAKTVNYTDATGATKTGAVKFGGANGKTEVVTTVDGNTYQASDVKGHNFQSGGALSEAVTTKTENPLAKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>b__Salmonella.enterica__Paratyphi.B__AY353359__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLSVQDAYTPKGTAVTRDVTTYKNGGTTLTAPNAAAIDTALGTTGAAGTAAVKFKDGNYFVEVTGTTKDGLYEATVDAAGAVTMTANKATVTGASTVTENQIVDAVTPTPVDTVAAATALTNAGVTGATGNTSLVKMSFEDKNGKVTDAGYALKVGNDYYAADYDEKTGEIKAKTVNYTDATGATKTGAVKFGGANGKTEVVTTVDGNTYQASDVKGHNFQSGGALSEAVTTKTENPLAKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>b__Salmonella.enterica__Niederoderwitz__AY353360__b,d,j\r\n+MAQVINTNSLSLLTQNNLNK'..b'ITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>d__Typhistr__CAAX01000878__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANGTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKEISSKTLGLDKLNVQDAYTPKETAVTVDKTTYKNGTDPITAQSNTDIQTAIGGGATGVTGADIKFKDGQYYLDVKGGASAGVYKATYDETTKKVNIDTTDKTPLATAEATAIRGTATITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>d__Typhistr__AJXA01000113__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANGTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKEISSKTLGLDKLNVQDAYTPKETAVTVDKTTYKNGTDPITAQSNTDIQTAIGGGATGVTGADIKFKDGQYYLDVKGGASAGVYKATYDETTKKVNIDTTDKTPLATAEATAIRGTATITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>d__Typhistr__JABZ01000017__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANGTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKEISSKTLGLDKLNVQDAYTPKETAVTVDKTTYKNGTDPITAQSNTDIQTAIGGGATGVTGADIKFKDGQYYLDVKGGASAGVYKATYDETTKKVNIDTTDKTPLATAEATAIRGTATITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>d__Typhistr__AJTD01000160__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANGTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKEISSKTLGLDKLNVQDAYTPKETAVTVDKTTYKNGTDPITAQSNTDIQTAIGGGATGVTGADIKFKDGQYYLDVKGGASAGVYKATYDETTKKVNIDTTDKTPLATAEATAIRGTATITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>d__Typhistr__AJTE01000190__b,d,j\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANGTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKEISSKTLGLDKLNVQDAYTPKETAVTVDKTTYKNGTDPITAQSNTDIQTAIGGGATGVTGADIKFKDGQYYLDVKGGASAGVYKATYDETTKKVNIDTTDKTPLATAEATAIRGTATITHNQIAEVTKEGVDTTTVAAQLAAAGVTGADKDNTSLVKLSFEDKNGKVIDGGYAVKMGDDFYAATYDEKTGAITAKTTTYTDGTGVAQTGAVKFGGANGKSEVVTATDGKTYLASDLDKHNFRTGGELKEVNTDKTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>r__Virchowstr__ABFH02000002__r,i\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQQKYKVSDTAATVTGYTDSATAIDKSTFAASATTLGGTPAITGDLKFDDTTGKYYADVSGTTAKDGVYEVTVAADGKVTLTGTPTGPITAGFPSTATKDVKQTQQENADLTEAKAALTAAGVAAAGTASVVKMSYTDNNGKTIDGGLAVKVGDDYYSATQNKDGSISINTTKYTADDGTSKTALNKLGGADGKTEVVSIGGKTYAASKAEGHNFKAQPDLAEAAATTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>r__Weltevredenstr__ABFF01000030__r,i\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQQKYKVSDTAATVTGYTDSATAIDKSTFAASATTLGGTPAITGDLKFDDTTGKYYADVSGTTAKDGVYEVTVAADGKVTLTGTPTGPITAGFPSTATKDVKQTQQENADLTEAKAALTAAGVAAAGTASVVKMSYTDNNGKTIDGGLAVKVGDDYYSATQNKDGSISINTTKYTADDGTSKTALNKLGGADGKTEVVSIGGKTYAASKAEGHNFKAQPDLAEAAATTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/H_new_fljB_protein_database.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/H_new_fljB_protein_database.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,378 @@\n+>z35__Salmonella.enterica__IIIb.38:k:z35__AY353262__other.z35\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQKAYDVDSKAVTPPAKLDIAGLTGTAIKTGVDSATVDTGSIKDGKVYYNSTSKNYYVEVDFGTSADAAKSGYYKVNVADDGTVSMTASTTKEATTPTGITEVTQVQKPVAAPAAIQAQLTAAHVTGADTAEMVKMSYTDKNGKTIDGGYAVKVGDDYYAATQKKDGSFSINTTSYTAADGTSKTALNQLGGADGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Typhimurium__AY353264__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Heidelberg__AY353265__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDTTLTIQVGANDGEPIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Derby__AY353266__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Stanley__AY353267__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Typhimurium__AY353268__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Muenchen__AY353269__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n+>1,2__Salmonella.enterica__Litchfield__AY353271'..b'KNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>1,2__Typhimuriumstr__AMEE02000100__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>1,2__Typhimuriumstr__ATWR01000017__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>1,2__Typhimuriumstr__AMDZ02000041__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>1,2__Typhimuriumstr__AMEA02000051__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>1,2__Typhimuriumstr__AERV01000016__1\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVKDTAVTTKAYANNGTTLDVSGLDDAAIKAATGGTNGTASVTGGAVKFDADNNKYFVTIGGFTGADAAKNGDYEVNVATDGTVTLAAGATKTTMPAGATTKTEVQELKDTPAVVSADAKNALIAGGVDATDANGAELVKMSYTDKNGKTIEGGYALKAGDKYYAADYDEATGAIKAKTTSYTAADGTTKTAANQLGGVDGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSEARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>z6__Weltevredenstr__ABFF01000037__k,z\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDSLNVQKAYDVDSKAVTVAANLDITDLNKDAALKAGTGATTGTAAIKDGKVYYDSASKNYYVEVTGLTTPDDGKNGFYKVNVADDGKVSMTAGTAMEAGKPAGAVEVTKTQEEKNPLPLSTDLKTSLKSGGITDPEIAAAQVVKMSYTDKNGKTIDGGYAVKVGDNYYAATQKKDGSFSVNTTSYTAADGTTKTALNQLGGADGKTEVVSIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDALRSDLGAVQNRFNSAITNLGNTVNNLSSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS\r\n+>z53__IIIb.60:(k):z53__HM142067__other.z53\r\n+MAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTLGLDTLNVQKAYDVDSKAVTDAKTIDLSALNEAALKAGTTGTTGAPVVKDDKIYYDEASKNYYVEVDGFTTGDVGKNGFYKVTVDADGKATMAASTTMEAAKPAGAVEVTKTQTETPVKLSAALKKSLTDGGVDTAAAGTAQIVKMSYTDKNGKTIDGGYAVKVGDNYYAATQKKDGSFSVNTTSYTAADGTSKTALNQLGGADGKTEVVTIDGKTYNASKAAGHDFKAQPELAEAAAKTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSARSRIEDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLR*\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/H_newest_database.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/H_newest_database.fasta Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,802 @@\n+>fliC_f,g,s_Agona_AY353383\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTGCTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAGAACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTTGATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z4,z32_16_z4,z32_--str_ANHR01000045\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGCCTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGGCTCCGTCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGGGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\r\n+>fliC_i_4,[5],12_i_-str_ABAO01000026\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAACTGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTGACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACA'..b'GGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGCTGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTGTTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT\r\n+>fljB_1,2_Typhimuriumstr_AERV01000016\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAACAACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTGGTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGTGGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGCTGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTGTTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT\r\n+>fljB_z6_Weltevredenstr_ABFF01000037\r\n+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTTTTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGACAGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTGCAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCTGATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGAGGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCAAAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAAAATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/O_3,10_and_1,3,19_spe.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/O_3,10_and_1,3,19_spe.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>O_3,10_not_in_1,3,19 +TTTTATATTATATTTGGCAGAGTGTTAGTATAATTGTCATGTTCAGTTTGAGGTAATTTATGTACTAATTATCTTATATTGTAAATCATGTGCAATTATTTTCATATTTTTATATGAAAAACGTCCAGTATATATATTGAGAAACATTATTGTTATGGAGACATCATCGGAGTTATGATGGAAAAAAACTCTTTTCCCATAAGCCACGAACATTCCTTAACTATGGATTATGTTAAAGCTTTTGGTATGATTTTCGTATTGGTTGGGCATATAAATAATGACATATTTAATGTTTATTATGCCTATCTTTTCCATATGCCATTATTTTTCTTTATTGGTGGGGTTTTATATAAAGATACACGGTGTATAACAAATTTTACAGCGCATGTTATAAAAAAACAGTTACCTTATCTTATAGTAACTTATTTGATTATTGGTTCTATTGCATTATTAATTAATGTACGTTATGGAATACACACAGGTGATGCTTTTTCGACAGGACTATATGAAACGGTTAAACTTGCTATAAAATCAAATTTTCATAACAATAAAATGTTTCTAACAGGTTGGTTTCTGTTTGCTTATATATTTGTGAGCATTTTGTCGGTGATTATAATAAAAAGCATAAAACGGGTCGTTGTTAGCAATGCTTTATTATTATCGGTATTGGTGGCGATTAGTGTATTATTAATAACTGTCTCAATAACATATTTATCCCCTCAATATATTCTGGTAAAAGACTATAAGCTGAATTTTATATGCCAAGTGTTAACCGGTATGTCGTTTTATATTTTTGGATACGTGATCAGAAATCAGATATATAACTTATTAAATTTTTATGTTTTTATTTTATTAACTGTAATATTATATGTTTCGAAAAGTTATGGTTTCTCTACGCAGACAATTATGTCATGGAGTTATTATCCGGATGGGTTAATAATGTCTGTTATTAACGCGCTGATAGGTATTTATGCTGTGTTTTTTATCTCTCTATTAATTACAAGGGGAATGAAAGAAATTAAGCTGCTAAAAATGATAGGTCAGAATTCAAGAGCTATCATGGCATATCATTTACTTGTATATGTAATTTTAGATATAATTGCTTCAATTTTAGGTGATTATAGCCTATCGGGAACAGATGTATATGATAATCACTTTATCACTAAATGGTCCGTTCCTGTCTACATTGCATTAGGTTTGCTACTGCCTCTAATTTTTAGTATTCTGAAACAGAAAGTAATAGGGAAGATAAAATTTAAGCGGGATTTTAGAATCAATTAAAAGCTAATTTTAGCTTTAATGCAGCCTAATGTTTAAGTATTAATTTTTGGATAAATATCACATAATAGGTTACTCAGGAGATTTTTATTTAGTCTACCGACGCGTTCCCAGATAAGGATTCCGGTGTGTCGTAGGTAGAAATAGGTAATTAATGATTGTTTCTTCGGGCTTTAAGTCTGGGTTATCATATTATTCACTTTATCTCATTGGATATAGTTCCTATGAGTAACCACACCTG +>O_1,3,19_not_in_3,10 +acgagaagtactgaataataattgtatcaaatagcctgcgtaaaatctgaacgcatcaatcgctaccttaatatcatacctttgagttaacatactattcacctttaacctgccatgaccgtttgtggca |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/O_4_wzy_but_not_in_rfb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/O_4_wzy_but_not_in_rfb.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,21 @@ +>O_4_wzy +ATGCTAACCACATCATTAACGTTAAATAAAGAGAAATGGAAGCCGATCTGGAATAAAGCGCTGGTTTTTC +TTTTTGTTGCCACGTATTTTCTGGATGGTATTACGCGTTATAAACATTTGATAATCATACTTATGGTTAT +CACCGCGATTTATCAGGTCTCACGCTCACCGAAAAGTTTCCCCCCTCTTTTCAAAAATAGCGTATTTTAT +AGCGTAGCAGTATTATCATTAATCCTTGTTTATTCCATACTCATATCGCCAGATATGAAAGAAAGTTTCA +AGGAATTTGAAAATACGGTACTGGAGGGCTTCTTATTATATACTTTATTAATTCCCGTACTATTAAAAGA +TGAAACAAAAGAAACGGTTGCGAAAATAGTACTTTTCTCCTTTTTAACAAGTTTAGGACTTCGCTGCCTT +GCAGAGAGTATTCTGTATATCGAGGACTATAATAAAGGGATTATGCCATTCATAAGCTATGCGCATCGAC +ATATGTCCGATTCCATGGTTTTCTTATTTCCAGCATTATTGAATATTTGGCTGTTTAGAAAAAATGCAAT +TAAGTTGGTTTTTTTGGTGCTTAGCGCCATCTACCTTTTCTTTATCCTGGGAACCCTATCGCGAGGGGCA +TGGTTGGCGGTGCTTATAGTAGGTGTTCTGTGGGCAATACTGAACCGCCAATGGAAGTTAATAGGAGTTG +GTGCCATTTTATTAGCCATTATCGGCGCTTTGGTTATCACTCAACATAATAACAAACCAGACCCAGAACA +TTTACTGTATAAATTACAGCAGACAGATAGCTCATATCGTTATACTAACGGAACCCAGGGCACCGCGTGG +ATACTGATTCAGGAAAACCCGATCAAGGGCTACGGCTATGGTAATGATGTGTATGATGGTGTTTATAATA +AACGCGTTGTCGATTATCCAACGTGGACCTTTAAAGAATCTATCGGTCCGCATAATACCATTCTGTACAT +CTGGTTTAGTGCAGGCATATTGGGTCTGGCGAGCCTGGTCTATTTATATGGCGCTATCATCAGGGAAACA +GCCAGCTCTACCCTCAGGAAAGTAGAGATAAGCCCCTACAATGCTCATCTCTTGCTATTTTTATCTTTCG +TCGGTTTTTATATCGTTCGTGGCAATTTTGAACAGGTCGATATTGCTCAAATTGGTATCATTACCGGTTT +TCTGCTGGCGCTAAGAAATAGAATAAAAAAACGCGCTGATACTTATTACGGTATCAGCGCGTTTTCCATC +ATCAGGACTCAATCACTTATCAAACCAGTTTTTCATTTGTTCCTCGAAACGCTGCGCTACATTTTCCCAA +CTGTATTTTGA |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/ParaA_rfb.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,2 @@\n+>O-2_Paratyphi A_rfb_56126533_extracted_from_genome_(minor genetic variant of O9)\r\n+TTATTCCAACCATTCGGTATGGAAAATGCCTTCTTTATCAGTACGTTTATAGGTGTGCGCACCAAAGTAGTCACGCTGCGCCTGAATTAAGTTAGCTGGCAGTACTGCGGCGCGATAGCTGTCATAGTAGGCCACTGCCGCAGAGAATGTCGGCACCGGAATGCCGTTCTGCACCGCGTAAGCCACGACATCGCGCAGCGCCTGCTGGTACTCATCAGCAATTTTCTTGAAGTAAGGCGCTAACAGCAAGTTAGCGATATCGGCGTTTTCTGCGTAAGCATCGGTGATCTTCTGCAGGAACTGAGCGCGAATGATACAGCCCGCCCGGAAAATCTTAGCAATCTCGCCGTAGTTGAGATCCCAGTGATATTCATCAGACGCGGCGCGTAGCTGCGAGAAGCCCTGCGCATAGGAGACGATCTTGCCAAGATACAGCGCGCGACGCACTTTCTCGATAAATTCAGCTTTGTCGCCTGCCGGCTGCGCTTTCGGCCCGGAGAGCACTTTAGATGCGGCAACACGTTGCGCTTTCAACGAAGAGATGTAACGCGCAAAGACGGATTCGGTAATCAGCGACAGCGGTTCACCCAGATCCAGCGCGCTCTGGCTGGTCCATTTACCGGTCCCTTTGTTGGCGGCTTCATCAAGAATGACATCCACCAGGTAGTTTCCGTCTTCATCTTTTTTAGTGAAGATGTCTTTAGTGATGTCGATCAGATAGCTGCTCAGCTCGCCGTTATTCCACTCAGTAAAAGTGTTCGCCAACTCTTCATTGCTGAGATTCAGGCCGCCTTTCAGCAGGGAGTAAGCTTCAGCGATAAGCTGCATATCGCCATATTCAATACCATTGTGGACCATCTTGACGTAGTGACCAGCACCATCGGCGCCGATATAGGTCACGCACGGTTCGCCATCTTCTGCCACAGCAGCAATCTTCGTCAGGATCGGCGCCACCAGTTCATAGGCATCTTTCTGACCGCCAGGCATGATAGATGGCCCTTTCAGCGCGCCCTCTTCACCACCGGAAACACCGGTACCGATAAAGTTAAAACCTTCCGCAGACAGCTCGCGATTGCGACGGATTGTGTCCTGGAAGAAGGTGTTACCGCCATCAATAATGATATCGCCTTTTTCCAGATACGGTTTCAGCGAATCGATAGCTGCATCAGTACCTGCGCCCGCTTTCACCATTAACAGGATACGACGAGGCGTTTCGAGGGATTCAACAAACTCTTTCACCGTGTAATAAGGCACCAGCTTTTTGCCGGGATTCTCGGCAATCACTTCTTCGGTCTTTTCACGGGAGCGGTTGAAAACGGAGACGGTATAACCACGGCTTTCGATGTTGAGCGCGAGGTTGCGCCCCATCACTGCCATACCGACGACGCCGATCTGTTGCTTGGACATTATTAACAACCGTGATAAATGGTTGGTGATAAACATAATAACGGCAGTGAACATTCGAAGCGGCAAGTTGGCTGAAACGAGTGTTGACTGCCGTTTTAGTTTTGTATAAAGGGCTTAAGTAACAAGGGGTTATCTGGAGCATTTTAATGCTGATTTTATAAGATTAATCCTTGTTTCCGGATGCAATTAATAAGATAATTAGCGTTTAAGTTTTAGTGAGCTTTGCCCTGCTGGGCGAGGTTTGTAACAAGTCGATATGTACGCAGTGCACTGGTAGCTGATGAGCCAGGGGCGGTAGCGTGTGTAACGACTTGAGCAATTAATTTTTATTGGCAAATTAAATACCACATTAAATACGCCTTATGGAATAGAAAAGTGAAGATACTTATTACTGGCGGGGCAGGTTTTATTGGATCAGCTGTTGTTCGCCATATTATTAAGAATACACAGGACACTGTAGTTAATATTGATAAATTAACCTACGCCGGTAATCTTGAATCCCTTTCTGATATTTCTGAAAGTAATCGCTACAATTTTGAACACGCGGATATTTGTGATTCCGCTGAAATAACGCGTATTTTTGAGCAGTACCAGCCGGACGCGGTGATGCATTTGGCTGCGGAAAGTCATGTGGACCGTTCGATTACCGGGCCGGCAGCATTTATTGAAACCAATATCGTCGGCACCTATGTACTTCTTGAAGTTGCGCGTAAATACTGGTCTGCGCTTGGCGAAGATAAAAAAAATAATTTTCGTTTTCATCATATTTCCACTGATGAAGTTTACGGCGATTTACCGCATCCTGATGAAGTTGAAAACAGCGTTACGTTGCCGTTATTTACTGAAACGACGGCATATGCGCCAAGTAGCCCCTATTCTGCGTCAAAAGCATCCAGCGATCATTTAGTCCGTGCCTGGCGGCGTACCTATGGTCTACCAACGATCGTTACCAATTGTTCTAATAACTATGGCCCTTATCACTTCCCTGAAAAACTGATTCCGTTGGTCATTTTGAACGCACTGGAAGGAAAGCCTTTGCCAATTTATGGCAAAGGGGATCAGATTCGCGATTGGCTATATGTAGAAGATCACGCTCGCGCGCTTCATATGGTAGTGACTGAAGGCAAGGCAGGGGAGACTTATAACATTGGTGGCCACAATGAGAAGAAAAATCTCGATGTGGTATTTACCATCTGTGATCTGCTGGATGAGATTGTACCCAAAGCGACTTCTTATCGTGAACAAATCACTTATGTCGCGGATCGTCCGGGCCATGATCGTCGTTATGCCATTGATGCAGGTAAAATTAGCCGTGAATTAGGCTGGAAACCGCTGGAGACCTTTGAAAGCGGTATTCGTAAAACAGTGGAATGGTACCTTGCAAATACTCAATGGGTAAACAATGTTAAAAGTGGGGCGTATCAGAGTTGGATAGAACAGAACTATGAAGGACGCCAGTAATGAATATCTTACTTTTTGGTAAGACAGGGCAAGTAGGCTGGGAGTTGCAACGTTCTCTGGCGCCAGTGGGGAATCTGATTGCCCTGGATGTCCATTCAAAAGAGTTTTGCGGTGATTTTAGTAATCCGAAAGGCGTTGCCGAAACCGTTCGTAAGCTTCGTCCCGATGTGATTGTTAACGCAGCAGCACATACTGCAGTAGATAAAGCAGAGTCTGAACCAGAACTGGCGCAGTTGCTTAACGCCACCAGTGTGGAAGCCATCGCTAAAGCGGCCAACGAAATTGGCGCATGGGTAGTGCATTATTCAACCGATTATGTATTTCCTGGTACCGGCGATATCCCATGGCAGGAAACGGACGCTACGTCGCCGCTGAATGTCTATGGCAAGACCAAACTAGCGGGAGAAAAGGCCCTGCAGGATAACTGCCCTAAATACCTAATCTTCCGCACCAGTTGGGTTTATGCAGGTAAGGGCAATAATTTCGCAAAGACAATGCTTCGTCTGGCGAAAGAGCGTCAGACACTTTCAGTCATCAACGATCAGTACGGTGCGCCAACCGGTGCGGAATTACTGGCTGACTGCACGGCTCATGCGATCCGTGTGGCATTAAATAAACCAGAAGTCGCAGGTCTTTACCATCTGGTTGCCGGGGGAACTACAACCTGGCATGACTACGCGGCGTTAGTCTTTGACGAGGCGCGCAAAGCAGGGATAACGCTTGCGCTGACTGAGCTTAATGCTGTGCCGACCAGCGCCTACCCGACGCCGGCGAGCAGACCTGGTAATTCGCGTCTCAATACTGAAAAGTTTCAGCGTAATTTTGGCCTTATTCTGCCGCAATGGGAATTAGGAGTTAAGCGTATGCTGACTGAAATGTTTACGACGACGACCATCTGATAAATTTAAATGCCCATAAGGGCATTTTCTATGAATGAGAAATGGAAATGAAAACGCGTAAGGGCATTATTTTAGCGGGAGGCTCCGGCACTCGTCTTTATCCGGTGACCATGGCGGTAAGTAAGCAATTG'..b'TGATGTTATTCATTCATCAGGTATTGTGTTTGGAACGAGTGGGGCTCGCGGTCTTGTAAAAGATTTTACACCTCAGGTATGTGCTGCTTTTACGGTTTCATTTGTTGCCGTTATGCAGGAACATTTTTCCTTTGATACCGTAGCATTGGCAATAGATAATCGTCCAAGTAGTTATGGGATGGCTCAGGCGTGTGCTGCTGCATTGGCAGATAAAGGCGTTAACTGTATTTTTTATGGTGTGGTACCAACCCCGGCTTTGGCCTTTCAGTCTATGTCTGACAATATGCCTGCGATAATGGTTACGGGAAGTCATATTCCATTCGAGCGGAACGGCCTCAAGTTTTATCGTCCTGATGGTGAAATCACGAAACATGATGAGGCTGCGATCCTTAGTGTTGAAGATACGTGCAGCCATTTAGAGCTTAAAGAACTCATAGTTTCAGAAATGGCTGCTGTTAATTATATATCTCGTTATACATCTTTATTTTCTACTCCATTCCTGAAAAATAAGCGTATTGGTATTTACGAACATTCAAGCGCTGGGCGTGATCTTTATAAGCCTTTATTTATTGCATTGGGGGCTGAAGTCATTAGCTTGGGTAGAAGCGATAACTTTGTACCTATAGATACAGAGGCTGTAAGCAAAGAGGATCGGGAAAAAGCACGCTCATGGGCTAAAGAGTTCGATTTAGATGCCATATTCTCAACAGATGGGGATGGTGATCGTCCTCTTATTGCTGATGAGGCCGGTCAGTGGTTAAGAGGCGATATATTAGGTCTATTATGTTCACTTGCATTGGGGGCAGAAGCGGTCGCTATTCCTGTTAGTTGTAATAGCATAATTTCTTCTGGCCGCTTTTTTAAACATGTTAAACTTACGAAAATTGGCTCGCCTTATGTTATCGAAGCTTTTAATGAATTATCTCGGAGTTATAGTCGTATTGTCGGTTTTGAAGCCAATGGCGGTTTTTTATTAGGAAGCGATATCTGTATTAACGAGCAGAATCTTCATGCCTTACCAACTCGTGATGCTGTATTACCAGCAATAATGCTGCTTTACAAAAGTAGGAATACCAGCATTAGCGCTTTAGTCAATGAACTCCCAACTCGTTACACCCATTCTGACAGATTACAGGGAATTACGACTGATAAAAGTCAATCCTTAATTAGTATGGGCAGAGAAAATCTGAGCAACCTCTTAAGCTATATTGGTTTGGAGAATGAAGGTGCAATTTCTACAGATATGACAGATGGTATGCGAATTACCTTACGTGATGGATGTATTGTGCATTTGCGCGCCTCTGGTAATGCACCTGAGTTACGCTGCTATGCAGAAGCTAATTTATTAAATAGAGCTCAGGATCTTGTAAATACAACGCTTGCTAATATTAAAAAACGATGCTTGCCGTAAAAGAATTGAATGTTATTTACTTAATATGCCTATTTTATTTACATTATGCACGGTCAGAGGGTGAGGATTAAATGGATAATATTGATAATAAGTATAATCCACAGCTATGTAAAATTTTTTTGGCTATATCGGATTTGATTTTTTTTAATTTAGCCTTATGGCTTTCATTAGGATGTGTCTATTTTATTTTTGATCAAGTACAGCGATTTATTCCTCAAGACCAATTAGATACAAGAGTTATTACTCATTTTATTTTGTCAGTAGTATGTGTCGGTTGGTTTTGGATTCGTTTGCGACATTATACATACCGCAAGCCATTTTGGTATGAGTTAAAAGAAATTTTTCGTACGATAGTTATTTTTGCTATATTTGATTTGGCTCTGATAGCGTTTACAAAATGGCAGTTTTCACGCTATGTCTGGGTGTTTTGTTGGACTTTTGCCATAATCCTGGTGCCTTTTTTTCGCGCACTTACAAAGCATTTATTGAACAAGCTAGGTATCTGGAAGAAAAAAACTATCATCCTGGGGAGCGGACAGAATGCTCGTGGTGCATATTCTGCGCTGCAAAGTGAGGAGATGATGGGGTTTGATGTTATCGCTTTTTTTGATACGGATGCGTCAGATGCTGAAATAAATATGTTGCCGGTGATAAAGGACACTGGGACTATTTGGGATTTAAATCGTACAGGTGATGTCCATTATATCCTTGCTTATGAATACACCGAGTTGGAGAAAACACATTTTTGGCTACGTGAACTTTCAAAACATCATTGTCGTTCTGTTACTGTAGTCCCCTCGTTTAGAGGATTGCCATTATATAATACTGATATGTCTTTTATCTTTAGCCATGAAGTTATGTTATTAAGGATACAAAATAACTTGGCTAAAAGGTCGTCCCGTTTTCTCAAACGGACATTTGATATTGTTTGTTCAATAATAATTCTTATAATTGCATCACCACTTATGATTTATCTGTGGTATAAAGTTACTCGAGATGGTGGTCCGGCTATTTATGGTCACCAGCGAGTAGGTCGGCATGGAAAACTTTTTCCATGCTATAAATTTCGTTCTATGGTTATGAATTCTCAAGAGGTACTAAAAGAACTTTTGGCTAACGATCCTATTGCCAGGGCTGAATGGGAAAAAGATTTTAAACTGAAAAATGATCCTCGAATCACAGCTGTAGGTCGATTTATACGTAAAACTAGCCTTGATGAGTTGCCACAACTTTTTAATGTACTAAAAGGTGATATGAGCCTGGTTGGACCACGACCTATCGTTTCGGATGAACTGGAGCGTTATTGTGATGATGTTGATTATTATTTGATGGCAAAGCCGGGCATGACAGGTCTATGGCAAGTGAGTGGGCGTAATGATGTTGATTATGACACTCGTGTTTATTTTGATTCCTGGTATGTTAAAAACTGGACGCTTTGGAATGATATTGCCATTCTGTTTAAAACAGCGAAAGTTGTTTTGCGGCGAGATGGTGCGTATTAAGCTCACCGAGAAGTACTGAATAATAATTGTATAAAATAGCCTGCGTAAAATCTGAACGCATCAATCGCTACCTTAATATCATACCTTTGAGTTAACATACTATTCACCTTTAACCTGCCATGACCGTTTGTGGCAGGGTTTCCACACCTGACAGGAGTATGTATTATTCATGCAAAAGCTGCTCTATGCTCTTACGGAACTTGGCTCCTTCTTTCAGGTTGCGCAGCCCGTACTTCACAAATGCCTGCATGTAGCCCATTTTTTTACCGCAGTCATAGCTGTCACCCGTCATTAGCATCGCGTCAACCGACTGTTTTTTCGCCAGTTCAGCAATGGCATCGGTGAGCTGGATGCGGCCCCAGGCGCCCGGTTCGGTTCTTTCCAGTTCCGCCCAGATGTCGGCTGAAAGCACATAACGGCCTACCGCCATCAAATCGGAATCCAGCGTCTGCGGCTGATCCGGTTTTTCGATAAACTCCACAATCCGGCTGACTTTGCCTTCATTATCCAGAGGTTCTTTCGTCTGGATAACGGAATACTCCGATAAATCACCTTTCATGCGCTTCGCCAGCACCTGGCTGCGACCCGTTTCATTGAAACGCGCCACCATCGCCGCAAGGTTATAGCGCAGCGGATCGGCGGTAGCATCATCGATAATAATATCCGGGAGTACCACAATGAAAGGGTTATCGCCCACGACCGGACGCGCGCACAGAATAGAATGCCCCAGCCCTAACGGCTGCGCCTGGCGAACGTTCATAATCGTCACGCCCGGTGGGCAGATAGATTGCACTTCCGCCAAAAGCTGACGCTTAACGCGCTGCTCAAGAAGTGATTCAAGTTCATAAGAGGTGTCGAAGTGGTTCTCAACGGCGTTTTTAGACGCGTGAGTCACCAGCACGATTTCTTTGATCCCTGCAGCCACAATCTCATCGACAATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTTGGGATTGCCTTGGTGGCAGGCAACATATGCATACCCAAACCCGCTACCGGTATAACTGCTTTCAAATTCATCAT\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/ParaA_rfb.fasta.amb Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +27467 1 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/ParaA_rfb.fasta.ann Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +27467 1 11 +0 O-2_Paratyphi A_rfb_56126533_extracted_from_genome_(minor genetic variant of O9) +0 27467 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta.bwt |
| b |
| Binary file SeqSero/database/ParaA_rfb.fasta.bwt has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta.pac |
| b |
| Binary file SeqSero/database/ParaA_rfb.fasta.pac has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/ParaA_rfb.fasta.sa |
| b |
| Binary file SeqSero/database/ParaA_rfb.fasta.sa has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/Typhimurium_LT2_gnd_galF.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/Typhimurium_LT2_gnd_galF.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Typhimurium_LT2_gnd +TTATTCCAACCATTCGGTATGGAAAATGCCTTCTTTATCAGTACGTTTATAGGTGTGCGCACCAAAGTAGTCACGCTGCGCCTGAATTAAGTTAGCTGGCAGTACTGCGGCGCGATAGCTGTCATAGTAGGCCACTGCCGCAGAGAATGTCGGCACCGGAATGCCGTTCTGCACCGCGTAAGCCACGACATCGCGCAGCGCCTGCTGGTACTCATCAGCAATTTTCTTGAAGTAAGGCGCTAACAGCAAGTTAGCGATATCGGCGTTTTCTGCGTAAGCATCGGTGATCTTCTGCAGGAACTGAGCGCGAATGATACAGCCCGCCCGGAAAATCTTAGCAATCTCGCCGTAGTTGAGATCCCAGTGATATTCATCAGACGCGGCGCGTAGCTGCGAGAAGCCCTGCGCATAGGAGACGATCTTGCCAAGATACAGCGCGCGACGCACTTTCTCGATAAATTCAGCTTTGTCGCCTGCCGGCTGCGCTTTCGGCCCGGAGAGCACTTTAGATGCGGCAACACGTTGCGCTTTCAACGAAGAGATGTAACGCGCAAAGACGGATTCGGTAATCAGCGACAGCGGTTCACCCAGATCCAGCGCGCTCTGGCTGGTCCATTTACCGGTCCCTTTGTTGGCGGCTTCATCAAGAATGACATCCACCAGGTAGTTTCCGTCTTCATCTTTTTTAGTGAAGATGTCTTTAGTGATGTCGATCAGATAGCTGCTCAGCTCGCCGTTATTCCACTCAGTAAAAGTGTTCGCCAACTCTTCATTGCTGAGATTCAGGCCGCCTTTCAGCAGGGAGTAAGCTTCAGCGATAAGCTGCATATCGCCATATTCAATACCATTGTGGACCATCTTGACGTAGTGACCAGCACCATCGGCGCCGATATAGGTCACGCACGGTTCGCCATCTTCTGCCACAGCAGCAATCTTCGTCAGGATCGGCGCCACCAGTTCATAGGCATCTTTCTGACCGCCAGGCATGATAGATGGCCCTTTCAGCGCGCCCTCTTCACCACCGGAAACACCGGTACCGATAAAGTTAAAACCTTCCGCAGACAGCTCGCGATTGCGACGGATTGTGTCCTGGAAGAAGGTGTTACCGCCATCAATAATGATATCGCCTTTTTCCAGATACGGTTTCAGCGAATCGATAGCTGCATCAGTACCTGCGCCCGCTTTCACCATTAACAGGATACGACGAGGCGTTTCGAGGGATTCAACAAACTCTTTCACCGTGTAATAAGGCACCAGCTTTTTGCCGGGATTCTCGGCAATCACTTCTTCGGTCTTTTCACGGGAGCGGTTGAAAACGGAGACGGTATAACCACGGCTTTCGATGTTGAGCGCGAGGTTGCGCCCCATCACTGCCATACCGACGACGCCGATCTGTTGCTTGGACAT +>Typhimurium_LT2_galF.fasta +TTATTCATGCAAAAGCTGCTCTATGCTCTTACGGAACTTGGCTCCTTCTTTCAGGTTGCGCAGCCCGTACTTCACAAATGCCTGCATGTAGCCCATTTTTTTACCGCAGTCATAGCTGTCACCCGTCATTAGCATCGCGTCAACCGACTGTTTTTTCGCCAGTTCAGCAATGGCATCGGTGAGCTGGATGCGGCCCCAGGCGCCCGGTTCGGTTCTTTCCAGTTCCGCCCAGATGTCGGCTGAAAGCACATAACGGCCTACCGCCATCAAATCGGAATCCAGCGTCTGCGGCTGATCCGGTTTTTCGATAAACTCCACAATCCGGCTGACTTTGCCTTCATTATCCAGAGGTTCTTTCGTCTGGATAACGGAATACTCCGATAAATCACCTTTCATGCGCTTCGCCAGCACCTGGCTGCGACCCGTTTCATTGAAACGCGCCACCATCGCCGCAAGGTTATAGCGCAGCGGATCGGCGGTAGCATCATCGATAATAATATCCGGGAGTACCACAATGAAAGGGTTATCGCCCACGACCGGACGCGCGCACAGAATAGAATGCCCCAGCCCTAACGGCTGCGCCTGGCGAACGTTCATAATCGTCACGCCCGGTGGGCAGATAGATTGCACTTCCGCCAAAAGCTGACGCTTAACGCGCTGCTCAAGAAGTGATTCAAGTTCATAAGAGGTGTCGAAGTGGTTCTCAACGGCGTTTTTAGACGCGTGAGTCACCAGCACGATTTCTTTGATCCCTGCAGCCACAATCTCATCGACAATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTTGGGATTGCCTTGGTGGCAGGCAACATATGCATACCCAAACCCGCTACCGGTATAACTGCTTTCAAATTCATCAT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/complete_oafA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/complete_oafA.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>oafA +ATGATCTACAAGAAATTCAGACTCGATATAAATGGGCTAAGAGCTTTTGCATTGATAAGTGTTGTGCTGTATCACTTCGGTGTACCTTATGTGTCAGGTGGCTTTATAGGTGTAGATGTTTTCTTTGTAATTTCTGGTTTTCTTATGACTGGAATTGTCCTTGAACGCGTAGACCACAAAGGAGTACTTGATTTTTATATTGCAAGATTCCTAAGAATTGTACCAGCTCTGGTATTTGCAATTCTCTTGTTGATGATTTTCGGTTTATTTACACTAAGTACAAATGAATACGAAGCACTTAGCAAGAACGCAATATCGTCTTTACTTTTTTATTCAAATAATTATTACGCAATTCACTCTAGTTATTTCGACTCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATTAGTCATTATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCGAGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACATAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTCGTGTTGTTATACTCGACAGTAATGGTTACTGGCCAAGCTATTCAGCACTCGCTCCCGTGCTGGGTGCTTCGATGGTTATTCTGGCTAACAAACAGAACTCTTTATTCACATCAAACAGAATTGCACAGTGGGTGGGTAAGATTTCTTACTCAGTTTATTTATGGCACTGGCCTGTAATTGTAGCGATGAAACATTATGATATTGAGTTCAGCGCTATAAATATTTTCTTTGGTGTAATTGTGTCTTTTGCGCTTGGGGATATTTCAGACAGAACAATTGAAAACACGCTCAGGAAACGAGTTAAGCTACAATTTAATATTGTATTATTTTCCTCTACTCTGGCTCTATGCTTGTTTGTCATGTTCACAAAAGGTGTTAGTTTTAGATTTTCAGACACCCTAAAGCAAGTCGTTGAGTATCGTATGGACAACTCTCCCTGGAGGCCTGATATTTGCTTCCTCAATCCAGATCAAGATTATTCAGCATTCTCAAAATGTCAGGATAAAATGACTGAAAAGTCTTTTGTTGTATGGGGTGACTCGCATGCCGCACATCTTATGCCAGGGCTGAAATCGGTATTTGGAAATTCACTTAACATTACGCAGAGAACTGCAAGCTTGTGCCCACCAATCATTGGGCTTCAAAAAGATGACAGGCCGTATTGCAAAGACATCAATGATATGGTAGCCAAGGAAATTTCAGACAACAAGCCTACTACGGTATTAATGTCCGCGTTGTGGCCTGTCTATCCTATGCGTGATTATCTGCCTGAGACTATTAAATTCCTGAAGGATAACAAAGTAAAAAACATCATCATTGTTGGCCCGTTCCCGGTTTGGAAGAAAACGATGATTGATACTATTGAGGATATGGGGATTAATTCCGGAAGGACCGTTCCATGGAGCATGACGGATGAAACCCGTAATCTGAGAGATAATGACAAATATCTTAGAGAGCTGGCGAAAGAGCATTCCCTTACTTATATTTCACCACTTGAGACTATGTGTACAGAAAGTTATTGCAAAGCAATAATAGGGAATAGAATTGCTTACCCTATACAATATGACAATGCGCACCTAACACCAGAAGGCTCAGGGTGGTTTATTGAGGAAGTGAGAAAGCAGATTTCAAAATAA |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_b_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_b_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fliC_b_Salmonella.enterica_IIIb.(6),14:b:e,n,x,z15_AY353362 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTACCAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTACGACTGGTGCGGCGGGTACTGCGGCAGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAGCTAAAGATGGTCTGTATGAAGCGACAGTTGATACAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGCACAGTTACCGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGTTAATTATACTGACGCTACTGGTGCAGCAAAAACTGGTGCTGTGAAATTTGGTGGTGCGAATGGTAAGACTGAAGTTGTGACCACAGTTGATGGTAATACTTATCAAGCTAGTGATGTTAAAGGACATAATTTCCAGAGTGGCGGCGCTTTAAGCGAGGCTGTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGATTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_d_Salmonella.enterica_Virginia_AY353372_b,d,j +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTCTGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTAAAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_k,z_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_k,z_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fliC_z_Salmonella.enterica_Indiana_AY353468 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGACTGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCGCGAATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTGGCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGCGTCGATGCTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAATACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_Blockley_AY353442 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAACAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCCTCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAAAATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGCAAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAGCTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATTGATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGCCACTGAATATACCGATAAAGACGGCAACACAAAAACTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_l_z13_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_l_z13_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>fliC_l,z13_Salmonella.enterica_Westerstede_AY353450 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAAAAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAAAGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACGAAAAATAAAGATGGATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCTCTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCACAACTTTAAAGCACAGCCAGAGCTGGCGGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_r_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fliC_r_Salmonella.enterica_Heidelberg_AY353459 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAACTGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTCCTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGATGGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTTCCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.61:i:z_AY353417 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACGGCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAACTGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAGACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACTGGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCTTGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAGCCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCCTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_r_whole.fasta.amb Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +2970 2 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_r_whole.fasta.ann Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,5 @@ +2970 2 11 +0 fliC_r_Salmonella.enterica_Heidelberg_AY353459 (null) +0 1482 0 +0 fliC_i_Salmonella.enterica_IIIb.61:i:z_AY353417 (null) +1482 1488 0 |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta.bwt |
| b |
| Binary file SeqSero/database/fliC_r_whole.fasta.bwt has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta.pac |
| b |
| Binary file SeqSero/database/fliC_r_whole.fasta.pac has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_r_whole.fasta.sa |
| b |
| Binary file SeqSero/database/fliC_r_whole.fasta.sa has changed |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_z36,z38_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_z36,z38_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>fliC_z36,z38_Salmonella.enterica_IV.43:z36,z38:-_AY353486 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTCTGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTACGAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAGAATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACTGCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTCTTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAGAACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTGACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_z4,z23_family.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_z4,z23_family.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,92 @@\n+>fliC_z4,z23_Salmonella.enterica_IV.1,40:z4,z23:-_AY353492\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCCTCGGTAGTTGGTGATGTAAAAATTGCGGCCGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z4,z23_Salmonella.enterica_Ajiobo_AY353493\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCCTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z4,z23_Salmonella.enterica_Ekotedo_AY353494\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCCTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>'..b',9,12,46,27:z4,z24:1,5_AY353504\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTACTGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGTTGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCCTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAATTATCTTTGATAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCTACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAGTACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACTTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z4,z24_Salmonella.enterica_IIIa.53:z4,z24:-_AY353505\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTAGGCACCGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGCGCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTCAGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCTTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAATTATCTTTGGTAAAAGATGATAAAGGAAACTATCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCTACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTCACTTTAGCTGGTGGTGCTTCAACCCCAAGTGCGGTTGATACTTTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCTAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\r\n+>fliC_z4,z24_Albanystr_AOZW01000055\r\n+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTACTGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGCGCGTTAAACGAAATTAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGCCTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAATTATCTTTGGTAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCTACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAGTACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAATTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_z4z23_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_z4z23_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>fliC_z4,z32_Salmonella.enterica_Tallahassee_AY353507 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCCATTGCGCAGACGACTGAAGGCGCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTCCGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACGGGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTTCAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGCCTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCGGCTGCAGATAAATTATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGGCTCCGTCAGCAGTAACTACCTTATCACGTGAAGTGAAATTTGATGGGGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAAACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fliC_z58_k_special_sequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fliC_z58_k_special_sequences.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>fliC_z58_Salmonella.enterica_I.47:z58:-_AY353518 +GAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGAC +>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436 +GAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGAC \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/fljB_e,n,z15_whole.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/fljB_e,n,z15_whole.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>fljB_e,n,z15_Salmonella.enterica_Braenderup_AY353324 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTATCAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGATGCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCCAACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGAAAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGGTGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAGTTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/new_Oserotype.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/new_Oserotype.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,256 @@\n+>O-56_GU445925_Salmonella enterica strain G2471_rfb_complete_sequence\r\n+ATTGGTAGCTGTAAGCCAAGGGCGGTAGCGTGTGTAACGACTTGAGTACTTAATTTTTATTGGCAAATTAAATACCACATTAAATACGCCTTATGGAATAGAAAAGTGAAGATACTTATTACTGGCGGGGCAGGTTTTATTGGATCAGCTGTTGTTCGCCATATTATTAAGAATACACAGGATACTGTAGTTAATATTGATAAATTAACCTACGCCGGTAATCTTGAATCCCTTTCTGATATTTCTGAAAGTAATCGCTACAATTTTGAACACGCGGATATTTGTGATTCCACTGAAATAACGCGTATTTTTGAGCAGTACCAGCCGGACGCGGTGATGCATTTGGCTGCGGAAAGTCATGTGGACCGTTCGATTACCGGGCCGGCAGCTTTTATTGAAACCAATATCGTCGGTACTTATGTTCTTCTTGAAGTTGCGCGTAAATATTGGTCTGCGCTTGGTGAAGATAAAAAAAATAGTTTCCGCTTTCATCATATTTCAACTGATGAAGTTTACGGCGATTTACCACATCCTGATGAAGTTGGGAATAGCGTTACGCTGCCGTTATTTACTGAAACGACGGCATATGCGCCAAGTAGCCCCTACTCTGCGTCAAAAGCATCCAGCGATCATTTAGTTCGTGCCTGGAGGCGTACTTATGGTCTGCCAACGATCGTTACCAATTGTTCTAATAACTATGGTCCTTACCATTTCCCCGAAAAACTGATTCCGTTGGTCATTTTGAATGCACTGGAAGGAAAGTCTTTGCCAATTTATGGCAAAGGGGATCAGATTCGCGACTGGCTATATGTAGAAGATCACGCTCGAGCGCTTTATATTGTAGTGACTGAAGGTAAGGCAGGAGAGACTTATAACATTGGTGGACACAATGAGAAGAAAAATCTCGATGTAGTATTTACCATCTGTGATCTTCTGGATGAGATTGTACCCAAAGCGACTTCTTATCGTGAACAAATCACTTATGTCGCGGATCGTCCAGGTCATGATCGTCGTTATGCCATTGATGCAGATAAAATTAGTCGCGAATTAGGCTGGAAACCGCTGGAGACCTTTGAAAGCGGTATTCGTAAAACAGTGGAATGGTATCTCGCTAATACAAAATGGGTTGAAAATGTGAAAAGTGGCGCCTACAAAGCATGGATTGAGCATAATTATACAGATCGTTCGCATTTTTAAATTATAGAAAAATTATTGTATAATCAGGTGGATTAAATGATTAAATTAAATTGTCCAATTGTACCGAATGTAAAAAAATACATATCACTAATTGAAAAAATCAATGAGAATGGTTGGTATACAAACTTCGGACCAATGCATGAAGAATTAACAAATAGATTATCCTCTTATTTAGGCGTACAGAATCTATTGCTCGTGTCAAATGGTACATTAGCACTTCAGATAGCATACGAAACATTGGGGGTAAGGAGGGCAATTACAACGCCATATAGTTTTGTTGCAACAGCATCCACATTAGCTTGGCAAAATAAAGAAATATTATATTCCGATGTTGATGAAAATAATGGAAATATTTCTTTTGAGAAAACTCTTTGCTTATTGAACGAAAATGAAAATTATGACAGTGTTGTTGCAACACATGTTTTTGGGAACCCATGTGAAGTTAATAAATTTAACCTCATTAATAAAAAAATAAATATTATATATGATGCGGCTCATGCGTTTGGAGTTAAAATTGATGGTGAAAGTGTATTAAACTACGGGGATGCAAGTACAATAAGTTTTCATGCAACCAAAGTATTTCATACTATAGAGGGCGGGGGAATTGTATTCAAGAAAAAAGAACACTTTGACGAAGCTAAAAGAATGATAAATTTTGGAATTGAACTTGACAAAGGAATTAAGTCGATTGGTATTAATGCAAAGTTGAACGAATATCAGGCAGCTGCAGGGCTTGTCTTCTTGGATGATATTGATGAAATTCTTGAAAGAAGAGTAGAATTATTTGAGTTATATCGTAGATGCCTCTACGATATCATTGATATGCCTAAATGGTTAGATCAAGCAAGCTTGAATGGTGCATATATGCCAATTTTTTGTAAGAATGAAAACGAATTAATCTCTATGATGAATAATCTAGAAAAAAAAGGGATACAAACAAGAAGATATTTTTATCCTTCATTGAATAATGTGATTAAGGCTAATCAAGACAGTAATACTATGGTTTCTGATGCGTTAGCTAAACGTTCATTATGCCTACCATTACACTATTACATGACTAAAGAAGAAGTATTAGTTGTAGTTGATGCAGTTAAAAGTAGTCTGTCTTAAGAAGGGATGTTTATGAAAATAGGGATTATGCAACCATATTTTTTTCCATATATTGGCTATTTTCAACTCGCAAATGCCGTTGATAAATTTGTAATTTATGATGATATTCAGTATTCAAAGAATGGATGGATTCAGCGGAATAGATTGCTAGTTAATGGCCAGCCATCTACATTCAGTATTTCTTTAAAAAAAGATTCTGATTATTTAGATATAGTAGAACGAGAAATTTCTGATAATTTTGACAGGGCAAAACTATGTCGCCAAATAAAAGGAGGATATAATAAATCAGCGCACTTCAAAGAAATATATCCAATTATTGAAAAAATAGTAATGCATGATGATAATAACTTATTTCAGTACATAAAAAACTCAATTGATGAGTTGTTTAGTATAATGAATATTAATGCCAATATTATTGTGTCATCAAAATTAAATATATCAAGAGAATATAAATCGCAGGATCGTGTCATACAGACATGTTTAGCATTGAATGGAAATGAGTATATTAATCCACCGGGGGGAGTGGCTTTGTATGAAAATATAGAGTTTGAACGCGTGGGGTTGAAATTAAAATTTCTTGAACCTTCAATAGAGACATATCAACAATCAACAGAATCATTTGTATCACATCTATCAATTATTGATGTCTTAATGTGGAATGGAATTGATAAAACACAAAAAATGGTGCAGAAATATGGCTTCATATAAAATATATAACATTAACAATTTTTCAAAAGAGAAATTTATTGATCTAGTGAAGGAAAATGAAAATCAGTTTATTCCGCCTCTTTCACAGCGAGTTGAACTGGATAATTATTTAAATAAAATTCTAACTTCCGCTGAAAATTATATTTTATTTGATGATGGCTTACACACAATTGCAAGTGCTGTTTCGTGCTATGCCAATAATGGTAAATACGGTTTCATCACAATGGTTTTGACTGACTCGAGGTTTCGAGGGAAAGGTTATGCAGTAACCTTATTGAAGCATGTAATTGCTGATGTCTTCAGTCGGGGTTACTCAGAAATTAATCTTGAAGTTCATAAAGAAAATAATAGAGCCATAAAGTTATATAAAGAATTAGGCTTTGTATTTAATAGTTGTAATATCACTGACTATCGAATTATGACTTTGGTGGCGCATAGTGACTAGATTTTTCATTAATGTAATTGCAAACTATATCGGGCAATTATATATGGCAATTATTGGGATTGCTATTATTCCCATGTATTTATCTATGCTTGGGAGTGCAGGGTTTGGATTGGTTTCATTTTTTACATTGCTACAGACACTTTTGGTAGTACTGGATTTAGGAATTTCATCAACCCTTTCAAGGGAAGTCGCAATACTAAAAACGGAAAGCACCTATTTTTCCGTTTTTATTAAGATACTAACATTTGTAATGTTGTTGTTTGTTTTTGTCTCTATTATGATAACATTCATCATGTATATTTTTAGAGATACTATTGCAACAAAATGGCTAAATACCTCAGAGCTAAGTCTGAATGATGTAGAGTATTCATTAGCAATAATAGGTATTATAATTTCATTACGGTGGTGTGCGGGTCCTTTTAAAAGCGTCATCTTGGGTTGTGAAGAG'..b'ACTGTAGGGTTATATACTAGTTATTGATGGCGCTTGATTTATCAATAACAGAAGATCAGAATGCCTGCTATGAAAATCTTCATCACTGTCCAATAAAAAGTTAAACTTGAAGGCCTGTATGATTTCAGCTGCGGCAAAAAGGCTTGAGAACGTAAAACTATTCTACTTGCTTCTGAAGGCCGTATTTCTGGCTTGACGTTCAGACTTTGCCCTGTAGTAGATGACCGTCGATTATCAAGTCATCTAGTTTCTCTGCAGAGGTAAGGATAGTATGTCTCTGTTTTTATCATAAAAGTTGAGGGGCAGGATATTTTCTGATAAAGCAAAAATATTGTGCTAATTAATTCTTTTAAAAAAAGAGTTACTAAAGTTGTTTATTGTGAAATTTATTAATCCCCAAAGGATATTAAACATATCCAAATAATATAGCAGGAGAATTTTTTTGAACTATTTGTAATGATGGTTTTATAAGTTAATAAAAAATTTACTTTAGATAAATATCACGTGAGAAATGTATTATGAATATATTATCTATCATAAGTGACTAAAATGCCAGTAAAAACTAACAACTTTCTTTATTTCATAATGGTCATAAGTGCTACCATTTTTGCTGTTAAAATAGTGCCTTATTCGAATGACTATCAGGCATATATTGATTTATTCAAATATACAATTCAAGATCCTTCTTACGAGAGAATGGAAATTGGCTTTAAAAACCTTATTGGTTTTTCAAAATTTCTTGATTTGAATTTTGATGTATTATGGTTTTTAGTTGCTTTTATTTCTTTGTCGCTAAAATGTTATGTATTAAAATCCTATGATTCAGATATCCTTGTATTATTTTTGTTGTACTTTTTGTACGCTATATCATTATTAGCTTTACACGAAACCACACAGATACGAGCGGCTATTGCAATTGCTTTAGGTATAGCAGGCTTTCGATGTACGAATAAATTTGTTGGTATCTGTTTAATCCTTTCTTCTGTATTATTTCACTATTCAGCAATTTTATTTATTATTTTGTATACTTTGAGCTTTATAGTTAAACCGTATAAGTTCACATGGTTAATAGTTGTTGTTACTATGGCGATACTAATACCCTTGCTTCTGGAACAATACTCAGATCCATTAATTAGTATTAATCCATTATTTTCATTATATTTAGAAAACTCTGATAATGCCAAGGTAAATAAATTTTCTTTTACTTTAATTCTTGCTACAATATTTTTTGTAATAAATTTTTTTATTGGAAGAAAAATTAACTATTATAGCAATAATAATTTCATATTTAAGCAATATAATCTTTTTTCTTTTCTTTATCTTTCTAGCGTAGTACTTTTATCTGCGTTGTCTTTTTCGCCAGTCATTTCAATAAGATTATATGAGTTATTTTCGTTAAGCCCTTTTATTATTATCGCATGCCTTTATTCTAAAAGTATGAAATACGTTTTTTATTCTAATATAAATTTGCGCTTGCTAAGAAGAGTTTTGCTTTTAACATTATGGCTAATCTCAGTGCATCGCTTTATTGCTTATTACTTTGTTAATCCAATCATTAAATTTTAAATTAAATGATAAAAAGGAATTATAACGTGTCCTCTAATAATGTTCCGTATATAGCCGCAGTTCTTGTAACGTTCAACCCAGACTTAAATATTTTCCAGGAAGTAATAAATACTATATCATCACAGGTGCAACATCTTATTGTTATCGATAACTGCTCCAAAAACAGGCTTGATATAAGCCTGTTTTTAAATGGAAAAGAAGGAGTGGTTTTATTACCTCAAAACAATAATATAGGATTAGCTGCGACACAAAATATTGGCATTCAATATGTTAAAGAAAATATTAATGCGACCCATGTAATTTTATTCGATCAGGATAGTATTATTAAACCATATTTTATTTCAAATTTAGTAAATGAAGAACTAGGGTTAATTAGTAAAGGGATTAAAGTAGGTGCAATTGGACCTAGCTTTTATGATCCCGACAATAATCAAGATTATCCTGCCACTGTCTATATTGGACCTTTTATAAAACGCGTTAAACTTGGAGACAATCCAGTTGAAGCCACTTTTTTGATTGCTTCGGGGTGTTTGATTAATCTGAATGTATTAAAAAACGTAGGTGGTATGCTTGAAGAGCTATTTATTGATTATATTGATGTTGAGTGGTCATTAAGAGCAAAGAAGTTCGGTTACAGGTTATTTATTACTCCCAAAGCATCAATGGCACACACTATAGGTGATAAGAGAATTTCTTTATTTGGACGTACTGTCTCTTGTCACAGTTCATTTCGACGTTATTTTCTTGTACGAAATAGTTTCAAAATGCTAAGGTTGCCTTATATACCTATTGGCTATAAAGTTCGTGAGACTGTATTCAATTTTCTAAGAGTTATAATTGGTCTAGCGACAAGTTCAGATAGGAAAAAGTTTATTAAATATACACTCGCCGCTTTTAAAGACGGTTTTTTTGGAAAATTTGGACCTTGTAAGTATAATTTTTAAAATGATTAAAATTGCACACATACAACTTCTTCCACTATTAAGTGGTGTCCAGCGAGTTTGTCTTGATGAATTAATTCGTCTTGATGAAAATAAATTTGATAAATATCTAATATGCAAAGAGGAAGGTCCTTTAACTGTTGAAGCAAAAAAATATGGCATAAAATGTTTAATGGTACGAAATCTCGTTAGAGAGATTTCGCTAAAAAATGATCTAAAAGCACTTTGGTCTTTATGGAAAATTATTAAGCAATATAAGTTTGATATTGTTCACACTCATTCATCTAAAACTGGAGTGCTTGGACGAGTTGCTGCATGGCTAAATCGTACGAACCTAATAGTTCATACTGTACATGGCTTCTCTTTTCCAATTGCTAAAAATAAGCAACAGAGAATATTATTTTGGCTAATGGAGAAGATTGGTTCTATGTGTGGAGATATTATAATTTGTTTACATGAAGATGATGCTAAAATAGCTCAGTCAATTCTTAAGATCAATAAGCATAAAATATGTATAATAAGTAATGGCGTCGATATCGAAAAGTTTAAACCTTATGATGAGGGTAGGAAATTTCTTTGTCGGGAAAATATTAAAGGTATTGATAGTGACGATATAATAATTGGAATGATAGGACGTCTTTGGCCACAAAAAAATCCAATATGTTTACTGCGTGCAGTTGCGGAAATAATAAAGAGTAATAAAAAAGTAAAGTGTTTTTTTATTGGTGACGGTGAGTTATATGGAGAAATGGCCCACTTCATTAAATCTAATCATCTTAGTAATAACGTGCAGTTATTTGGGTGGCGTAATGATACGCATACTTTTCTTAATGCAATGGATATTTTTGTTTTGCCATCCCTTTGGGAAGGGATGCCTTTAGCCATTCTGGAAGCCAAAAGTTGTGGCCTTCCCTGTGTTGTCTCCAATATACAAGGGAATCGTAGTATTATTGACGGTGTCGAGGATGGGTTGTTATTCGATTTGGATTTGAGTTGGCATGACTTATATGAAAAATTACAATTGCTTATTGGAGATTCTCAGTTAAGGAGTATTATCGGTAAAAAAGCCCGATTGAGTATAATAAATCATTATAATATTGCTTCCAGAATTAAGAAAATCGAGAGGATGTATCTGAGGAAAATTAAAAAACATTCTCACGTTAATTCTTAAAAGATGTATTCTTTCATAAGCTAAAGTAGCATAATTTTATGGTTTGCCGTAATTAATATTTAGCCTCGACTTAGATGTGATTTTTATTTTAGACATTATAGTGGGGCAGAGATAAAATATGATCAGTTCGCTGAATTAATCTTATTAAGAACTCAATTTTTTATTGAAGACTCAAAATTATATAAATTATACTGTCATTAATTACTATTTTTAAGTTATTATTTAAGGGTTTCAAACCGTGTCTACCTGGCGCGGTGACCACACCTGACAGGAGTATGTAATGGCCAAGCAACAGATCGGCGTCGTCGGTATGGCAGTG\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/oafA_of_O4_O5.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/oafA_of_O4_O5.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>O-4_full +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATTAGTCATTATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCGAGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACATAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTGCTGTTGTTAT +>O-4_5- +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATCCTTTATTAGTCATTATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCGAGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACATAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTGCTGTTGTTAT \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/special_O_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/special_O_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,139 @@\n+>O_1,3,19_not_in_3,10\r\n+acgagaagtactgaataataattgtatcaaatagcctgcgtaaaatctgaacgcatcaatcgctaccttaatatcatacctttgagttaacatactattcacctttaacctgccatgaccgtttgtggca\r\n+>O_11_wzy\r\n+ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGTTATTATTTTCCCTCGCATATAAAAATAAAAATA\r\n+AAAATATAAATGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGCCTTAGAGTTAA\r\n+TGATAGTGATTATCTTGAGTATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCT\r\n+GCGATAAAAGATATTCATGGAGAGATTGGCTATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATTTAC\r\n+CGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTTGATGCTTACTTATTTTTCTTTTAAAAAAGC\r\n+AAGTATTATACCAATATTATCTCTAGTTTTTTATTTAAGTCATGCTTTTATTGTTAGGGATATGATACAA\r\n+ATAAGAGCTGGATTAGCGGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAAAATCGAAATGTGA\r\n+TCACAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTAT\r\n+AAGAAAAAGATATTTATCGTTAAAAAAAATATTTTCTCTTTTCTTGGTTGCCTTAATATTTTCTTATTTA\r\n+CATGGGCTCGACTTTATATTAAACACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATA\r\n+TTGGGTGGGAAGAATATGATTATAGAATTAATATTTTCACTAATCCAGTATTTATTAAAGGGATAATGAT\r\n+AGTTTTTTTAATGAGAAAATATATTAAAACAAATATAAATAATGAAAATGATAAGGTGGTTATATTATAT\r\n+AATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGGTTAAGTGAGATGGCTATACTTTCAGGACGTCTTT\r\n+CATCGTTTTTAACACTAGGTGAAAGCATATTAATAGTATATAGTGTTTTTTATAAAAGAAATATCTCGGT\r\n+AGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTCAAACGTACAT\r\n+CCGAAGCTCTCTCTTTTTATATTTGGATAA\r\n+>O_13_wzx\r\n+ATGGAAAAGCGTATTTATATAAATACCATTGCTAATTTATGTGGGGTTTTTTGGCAGGGAGCTATAATTCTTTTAATGGCTCCTTTTTACCTGAAGTTATTAGGGAAAGAACAATGGGGTATGGTGGCTGCATGTTTATCCTTACAAGGGATATTATTACTGCTTGATGCAGGAATGTCACAAGTTATGCCAAGGGACTTTGCACAAAAAAAACAGAATATTAAAGAGATATATTCAAACTATATAGCTTTATATTTTTTGATTGCGCTTTGTGCTGTGTTTTTCTTGTATTTTTCTGCAGAGGCTATTGCTGAAAAATGGTTTAGATTGGATGCTTTTTCTGCAAAGCAACTTGAACTCGCTATAAAAATTTTTGCAGGGCAGTTTTTTTTCCAGTTTTGCAATAACGTTAATTTGGCATATTGGAATGGGAATGAAGAGCAAGTAAAAGCAAACTTATCGCAATGTATATTCATTTCTTTGAAAAATATTACAGCAGTAATTTTAATTCTAAACGTTAGCCGACAAACATATATTTATGTATTATCTTTCTTCCTAATTGCTATGATTGAGTTTATCTGTAATTTTTCTTTTATCGTATCAAGGATAGGAGCGTGTAAACCGTCATGGGGAAAAATCAAAAGAATTATTATTACTAACTATAAAATATCCTTAGGGATTCTGTTAGGCGTTTTTTCTTCACAATTAGATAGAATATTTATGTCAAGGTTTTTAAGCATTCAAAACTTTGGCTTGTATGTTATGACTATGCAATTTGGACTTGCGTTATTGCAGTTACAGTATCCAATGGTTAAAGCAATATTACCTCATATCGCAAAAATTGGCGATACAACTAAGTTGGGATTATATAAAACAATAGCTTTTTTTTGTGTCTTAATGCCATCTTGCATATTATTTTTTTGGGCAAAAGACATACTTTGGTTATGGAGTCATAATATTGAAGTTGTAGAGTATGGAGTTATTATTGTCAAAATTTTGAGCGTTGCTGTGCTGATAAACTTTTTTTATAACTTTATTCACGTTAAGTTAATTGTTGAAAATAGAGGTGGGGTGATATTTATTTCGCAACTTTTGATTATTATTATTAACTCTATTTTCCTAATATTCTTTTCCCCAAGAATTCATGAGGTGGCTGGAGCATTATCATGGATGATTAATTTTAGCATAGTCTTATTATGTGGTTTGTTTTTTCTCCATAAAGGAAAAAAAAGATAA\r\n+>O_16_wzy\r\n+ATGAATAACCAAGATTTAAAAATTGGTACTGCATTTATTTCAATGATTTATTTTCCCTTGGGATTTTTGG\r\n+TATCACTTATTGAAGTAATTAATGGATATAGGTGGGGAAACTTTCTATTCGCATTTATCTTGGGTCTATT\r\n+AGCATTCTCACTAATACCGTATAGTGATTGGGATCTAACAAGACATTATGAAACCTATTTAAGTTATAAT\r\n+AATACCTCTTTTAGTGAAGTATGGGAACAAAGTGATAATCGATATTTAGTAATAAATACTATAATTTATC\r\n+TATTTAATACTTTCGCTATCAAAAAGGAGTTTTTACCGTTCTTTGCTGTTTTTATATCTTATTTGTTTTA\r\n+CTTAAATGTATTTTCGAAATTTATTAGAGAAAAAAAGCCTAATATTTTAATCCGAAGCATCTATTTATAT\r\n+ATTTTATTAACGGTAATACCTTTTTTTGCTATAGCTAGTTCACTACGACAATATTTAGCCTTCAGTATTA\r\n+TATTATATATAATAATTACCTACTGTAGTAAGCAAGATAGACGTACTTTCCTTATATCTTTCCCACTAGT\r\n+TGTTATGGCAATAGGAATACATCCAAGCGTAATTCTGTTAATAGCACTGTTTCTATTTAGCAGATTTATA\r\n+CGCCTAAATCGAATAGTTGTGCTTCTTATTTTTTTCATATTAGTTCTAAATTTTAATGGTTATATTTCAA\r\n+TACAATTATTCAAGCTATTTAAACCATTATTAATGAATACAGGTTTTTATTATCCGGAATATATGGATGC\r\n+AGAGGTTATTCATATGAATAACCAACTATTAAGCACGAATGAATTTATACTTAATAAATTGATTTTACCC\r\n+AGTATATTTTATTTGTTAATCCCAGTCTTTTTGATTTTCTATAAAAAATCAAACAGTAAACAGGAAAAGC\r\n+AACTAAAAAACTATTGCGCACTACTCCTTTTGACTATATGCCTGTTATCTTTATCACCTGATCTTTTTTA\r\n+TCGATTTTCAATATTTTGGACATTATTCTATAGCTATATATATTTCACTTATGATAGTGAGAGAATGAGT\r\n+TTGCCTGCCAAACAGTGCTATCTTGTAATTATAATTGTTGCATCATGTGTCATAAACTTAGCTCAAGCTA\r\n+ATATGGGCAAGAAAATCATATATAATTCATGGGGATCATTTTTTTACCAACCTTCACTATTCGTGTTTGT\r\n+TAAAGAAATCAAAACGACTGACTATATAAATGTGAGCCAATAA\r\n+>O_17_wzx\r\n+ATGAAATTTTCCCATAATACTGTATTTTTTTATTTGTTAACTATCGTAAATGGTTTGGTTCCGTTAATAACAATTTCATTTATATCAAGGATAGTAACAAGTGAGCAGCTAGGTATCTATT'..b'TATGTATGGAGTGTTTTTCCCAAGGATATAAAAGATTATTGATGCTTATTATTAGTTTTGTGCTATTTATAGCGATCTGCATGAGTCTTACTAGAGGAGCAATACTTGTTGCTGCGCTTATTTACGCACTTTATATAATTTCAAATCGGAAGATGCTTTTTTGTGGAATAACTTTATTTGTAATAATTATACCCGTTTTAGCAATTTCTACTAATATTTTTGACAACTATACAGAAATTTTGATCGGCAGGTTTACAGATTCGTCTCAGGCATCGCGTGGATCTACACAGGGGCGGATAGATATGGCAATTAATTCATTAAACTTCCTGTCAGAACATCCATCAGGTATAGGTCTGGGTACTCAAGGTTCAGGAAACATGCTTTCGGTAAAAGATAATAGGTTAAATACGGATAATTATTTTTTCTGGATCGCCCTTGAGACTGGTATTATTGGCTTAATCATAAATATTATTTATCTGGCAAGTCAATTTTATTCTTCAACTTTACTAAATAGAATATATGGCAGTCATTGTAGCAATATGCACTATAGATTATATTTTCTCTTTGGAAGTATATATTTTATAAGTGCAGCGTTAAGTTCAGCACCTTCGTCATCAACTTTTTCTATATATTATTGGACAGTTTTAGCTTTGATTCCATTTTTAAAATTAACAAATAGACGGTGCACGCGATAA\r\n+>O_9,46,27_partial_wzy\r\n+ATGTTACCGCATACATTTATGTTCCTGATTTTTAATATAGTATATATGTTACCAGTAGCCTATGTACATTTTTTTGGGTTCTCCCTTGGAGGGGTTGAAGAGATTCTCAACGGTGATCCCAGTATGCTTGCAGATATGATGGTCTTTTACGTCGCTGTCTGGTTCTTTTATCTTGCCGGTTCGGCATTATTAGGATTTGGTATAAAAAATAAAAATATACAATGGATTATAGCATTCGAACTTCCAATTATTGTAAAGATTTTATTCAGTTTAGTTTTATTTTTTATAGTACTATCAAAAGTATTGCTTTATCCTGAAGGGGTTTACTCATCTTATGCCTTTGATTCTGGCGCTATGGCAAGTCGTGTCTGGAATATCTCGATGGGATTATCAGAACTAGGTATAATAATTTTTACATTTTGTTTAGTTACAAAGAATATAAAGTTTGCAGTTGTTACCTTTCTTATAGTCTCATTAAATCTACTACATGGGACTAGAATATTTACATTGATATTACTTTTAATGATCATATTTTATATAATTTTTATTAATAAAAAAATATCAAAGCTGAAATTATTTATTATTTTGAGCCTTTTTTTTGGCGCAATAGTGATATCATTTTTGATAATATTCATTATCCGTTCTAATGTTTCAATTGAAAATATAAATATAGACCTAATTCTAAGTCCAATAGTATATGAGTCTTTATTTAATCAAATATCTTTTATGCGGATGCTGGATTGGCTACATCAAGGGGCAGTTCCGTTTGCACCACAAATGCTTTTTTCTGATTCAGCTATATTTACGTTACCGACTTTTCTTTTTGATGAAAAATCATCTTTAATGTATATAAATAAATTTGGAGAACTTAGCCCTTTAGGTGGGCTTTCCGGTTATGCTAGTGCAGTAATATATTTTTCGTATTATTATTTCCTGTGGTATTTTATTCTCGGTATTACATCAAGCTTATTATTAAGGTTTACATCGAGTGTAAACTTTGTAATATTGTCGAGAGTTAT\r\n+>O_9,46_wbaV\r\n+ATGAAGGTATCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGACCTTCTTGAAAGTATTAATAATCAATCTTCTCACTCCTTAATTGTAGAAGTATGTATTTCAGATAATGCATCAACTGATGGAACTGAAGAGTCAATAAATATCTGGAGAGATAGATTTAATTTTCCAATTTTGTATCAAAGGCATAACGAAAATATTGGGCCAGATAGGAATTATTTATCTGCAGTTAATATGGGGACTGGAGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAATTCCCTTGCATTGATGGAAGATAAATTGGCTGCCGGAAGTGGCATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAAAATATCTAATCCACATCGGCGATGGTTAAATGGTGGCAGTAGATTATTTTCTTTTAGCAATGAAGCTGATTTGATAGAGTACTTTAGTAAATGTAACTCAGTCGGCGGACTTTTTAGCTACTTAAGCTCTATTATAGTGAAAAGGAATAAATGGTCTGACGTCATATTTGACGAGTCATACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTGCAGTACATATCACTGCCACTGGTTGATTGCAGAGGAAATAACGATACATTCGAAAGTAATGGGAAGGCTCGTCGAATAAAAATTGATTTCATCGGTTATTTAAAACTGAGGGAGGATTTTTATAATAACAATACAAAAATATATATCTCATTTGGACGGGTTCTTACAAAAGAGCGTCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACCGATAGGGCTGAACTTGCATCATTTTATAAGAAGTTGGGATATCCGAAAATAGCCACCAATTTAATATTTCGTCTTAAAGGGCTGGCTAGCTACACTAAAAAAATAAAATTAGCAAAAATGGTAATAAAAAAAATATTTTCATAG\r\n+>O_9,46_wzy\r\n+ATGAGATGTGCTATGGTATTTTTAGCGTGGTTTATTGCTATTGGGATATATATAATATGTGGTATTTTTTATCTTCAATTTCCTCAATTATCACCACTAGGGGCTCTTGCATATACTGATACAGTGGGCGATGTAATCATTGTCGTATCCACGGGGATAGTGGGAGTTTTTCTCGGCTATTTTGCATTTTCTAAAATCAAGTTAGTAGGAATAAAAGATTTTAATAATTCGTGTTTTATAAATTTTTGTTCAGTATGCTTTATTATTTCAGCGTTTCTAATTTTCGCCTTAGGCGTCGCTGCATATGGTGGTTACATAGCATTTCTACATACGCCTTATATAGCAATCTATGAAGGTAGTGCAGAAAATCAAACCAGAGATATCCTCATATCTTCATCGGGATTGCTTGCTAACTATGCACTATTAACTAGCATTCGTGTCAACTTTAAAGAAATATCAATAACTAATAAAGTTGTCATAGCAGTATCGCTATTAATACTTGTTTCTATATTTATTCAGGGACGAAGAGAAAATTTAATTTTGCTAATATTATGTTTCGTGTCATTCTATATGCTAAATTATAAAATTAATTTTAAACGTATTATCAAAGTAAGCATTATTTGTATAATAATGTTTTTCATTGCTGGATTAGGTTTATATTTGCGTGAAAGCACTTCAACTTCAGGAGGAAGTATTTTTACAGCTATACCTTTTGCCGTGATGTATGAAACACATTTTTCTTTAGCGACTTTGGCTAATGAAGTGAGAACGCATTTATATAATAATTTACCTTATGGGGGAGTATTAGATTTATTTTCTCCCATATTATTTATTATCCCTGCTTTTATATATGGGATTTTTGGTTTAGATAAACAATCTTTGTTCGAGAATAATGAGATGCGTTTTTATGAGGATAAAGGCGGCCAGTTTATATTCACAGAGGCTTTTCATTCACTTGGTTATGTCGGAGTATTCCTGCATGGTTTAATCTTGGGTGTAATGCTAATAGTATTTTATCGTGTAGCCAAGAAAAGCAGGCTCATAATTTATCATTTTCCAATTATTTCCCTCATATTTGTTGCAATGAGAAAAGACCTTACCTATGGTGTTAAATATATTTCTCTTTTGTTCATATTTATGATGATTTTTTATTTCATCTATAAGTTACTCCCACTTAAAAATAATGGTTGA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/special_new_O_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/special_new_O_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,160 @@\n+>O-1,3,19_not_in_3,10\r\n+acgagaagtactgaataataattgtatcaaatagcctgcgtaaaatctgaacgcatcaatcgctaccttaatatcatacctttgagttaacatactattcacctttaacctgccatgaccgtttgtggca\r\n+>O-11_wzy\r\n+ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGTTATTATTTTCCCTCGCATATAAAAATAAAAATAAAAATATAAATGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGCCTTAGAGTTAATGATAGTGATTATCTTGAGTATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCTGCGATAAAAGATATTCATGGAGAGATTGGCTATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATTTACCGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTTGATGCTTACTTATTTTTCTTTTAAAAAAGCAAGTATTATACCAATATTATCTCTAGTTTTTTATTTAAGTCATGCTTTTATTGTTAGGGATATGATACAAATAAGAGCTGGATTAGCGGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAAAATCGAAATGTGATCACAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTATAAGAAAAAGATATTTATCGTTAAAAAAAATATTTTCTCTTTTCTTGGTTGCCTTAATATTTTCTTATTTACATGGGCTCGACTTTATATTAAACACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATATTGGGTGGGAAGAATATGATTATAGAATTAATATTTTCACTAATCCAGTATTTATTAAAGGGATAATGATAGTTTTTTTAATGAGAAAATATATTAAAACAAATATAAATAATGAAAATGATAAGGTGGTTATATTATATAATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGGTTAAGTGAGATGGCTATACTTTCAGGACGTCTTTCATCGTTTTTAACACTAGGTGAAAGCATATTAATAGTATATAGTGTTTTTTATAAAAGAAATATCTCGGTAGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTCAAACGTACATCCGAAGCTCTCTCTTTTTATATTTGGATAA\r\n+>O-13_wzx\r\n+ATGGAAAAGCGTATTTATATAAATACCATTGCTAATTTATGTGGGGTTTTTTGGCAGGGAGCTATAATTCTTTTAATGGCTCCTTTTTACCTGAAGTTATTAGGGAAAGAACAATGGGGTATGGTGGCTGCATGTTTATCCTTACAAGGGATATTATTACTGCTTGATGCAGGAATGTCACAAGTTATGCCAAGGGACTTTGCACAAAAAAAACAGAATATTAAAGAGATATATTCAAACTATATAGCTTTATATTTTTTGATTGCGCTTTGTGCTGTGTTTTTCTTGTATTTTTCTGCAGAGGCTATTGCTGAAAAATGGTTTAGATTGGATGCTTTTTCTGCAAAGCAACTTGAACTCGCTATAAAAATTTTTGCAGGGCAGTTTTTTTTCCAGTTTTGCAATAACGTTAATTTGGCATATTGGAATGGGAATGAAGAGCAAGTAAAAGCAAACTTATCGCAATGTATATTCATTTCTTTGAAAAATATTACAGCAGTAATTTTAATTCTAAACGTTAGCCGACAAACATATATTTATGTATTATCTTTCTTCCTAATTGCTATGATTGAGTTTATCTGTAATTTTTCTTTTATCGTATCAAGGATAGGAGCGTGTAAACCGTCATGGGGAAAAATCAAAAGAATTATTATTACTAACTATAAAATATCCTTAGGGATTCTGTTAGGCGTTTTTTCTTCACAATTAGATAGAATATTTATGTCAAGGTTTTTAAGCATTCAAAACTTTGGCTTGTATGTTATGACTATGCAATTTGGACTTGCGTTATTGCAGTTACAGTATCCAATGGTTAAAGCAATATTACCTCATATCGCAAAAATTGGCGATACAACTAAGTTGGGATTATATAAAACAATAGCTTTTTTTTGTGTCTTAATGCCATCTTGCATATTATTTTTTTGGGCAAAAGACATACTTTGGTTATGGAGTCATAATATTGAAGTTGTAGAGTATGGAGTTATTATTGTCAAAATTTTGAGCGTTGCTGTGCTGATAAACTTTTTTTATAACTTTATTCACGTTAAGTTAATTGTTGAAAATAGAGGTGGGGTGATATTTATTTCGCAACTTTTGATTATTATTATTAACTCTATTTTCCTAATATTCTTTTCCCCAAGAATTCATGAGGTGGCTGGAGCATTATCATGGATGATTAATTTTAGCATAGTCTTATTATGTGGTTTGTTTTTTCTCCATAAAGGAAAAAAAAGATAA\r\n+>O-16_wzy\r\n+ATGAATAACCAAGATTTAAAAATTGGTACTGCATTTATTTCAATGATTTATTTTCCCTTGGGATTTTTGGTATCACTTATTGAAGTAATTAATGGATATAGGTGGGGAAACTTTCTATTCGCATTTATCTTGGGTCTATTAGCATTCTCACTAATACCGTATAGTGATTGGGATCTAACAAGACATTATGAAACCTATTTAAGTTATAATAATACCTCTTTTAGTGAAGTATGGGAACAAAGTGATAATCGATATTTAGTAATAAATACTATAATTTATCTATTTAATACTTTCGCTATCAAAAAGGAGTTTTTACCGTTCTTTGCTGTTTTTATATCTTATTTGTTTTACTTAAATGTATTTTCGAAATTTATTAGAGAAAAAAAGCCTAATATTTTAATCCGAAGCATCTATTTATATATTTTATTAACGGTAATACCTTTTTTTGCTATAGCTAGTTCACTACGACAATATTTAGCCTTCAGTATTATATTATATATAATAATTACCTACTGTAGTAAGCAAGATAGACGTACTTTCCTTATATCTTTCCCACTAGTTGTTATGGCAATAGGAATACATCCAAGCGTAATTCTGTTAATAGCACTGTTTCTATTTAGCAGATTTATACGCCTAAATCGAATAGTTGTGCTTCTTATTTTTTTCATATTAGTTCTAAATTTTAATGGTTATATTTCAATACAATTATTCAAGCTATTTAAACCATTATTAATGAATACAGGTTTTTATTATCCGGAATATATGGATGCAGAGGTTATTCATATGAATAACCAACTATTAAGCACGAATGAATTTATACTTAATAAATTGATTTTACCCAGTATATTTTATTTGTTAATCCCAGTCTTTTTGATTTTCTATAAAAAATCAAACAGTAAACAGGAAAAGCAACTAAAAAACTATTGCGCACTACTCCTTTTGACTATATGCCTGTTATCTTTATCACCTGATCTTTTTTATCGATTTTCAATATTTTGGACATTATTCTATAGCTATATATATTTCACTTATGATAGTGAGAGAATGAGTTTGCCTGCCAAACAGTGCTATCTTGTAATTATAATTGTTGCATCATGTGTCATAAACTTAGCTCAAGCTAATATGGGCAAGAAAATCATATATAATTCATGGGGATCATTTTTTTACCAACCTTCACTATTCGTGTTTGTTAAAGAAATCAAAACGACTGACTATATAAATGTGAGCCAATAA\r\n+>O-17_wzx\r\n+ATGAAATTTTCCCATAATACTGTATTTTTTTATTTGTTAACTATCGTAAATGGTTTGGTTCCGTTAATAACAATTTCATTTATATCAAGGATAGTAACAAGTGAGCAGCTAGGTATCTATTTATTATCATTTACGATAATGAATGTTTTAGGCTTAGTTATAGATTGGGGCTTTACAATATCTGGCATTAGATTTTTAAAAAATAGTAATAAAAAAA'..b'TTCAGGAAACATGCTTTCGGTAAAAGATAATAGGTTAAATACGGATAATTATTTTTTCTGGATCGCCCTTGAGACTGGTATTATTGGCTTAATCATAAATATTATTTATCTGGCAAGTCAATTTTATTCTTCAACTTTACTAAATAGAATATATGGCAGTCATTGTAGCAATATGCACTATAGATTATATTTTCTCTTTGGAAGTATATATTTTATAAGTGCAGCGTTAAGTTCAGCACCTTCGTCATCAACTTTTTCTATATATTATTGGACAGTTTTAGCTTTGATTCCATTTTTAAAATTAACAAATAGACGGTGCACGCGATAA\r\n+>O-9,46,27_partial_wzy\r\n+ATGTTACCGCATACATTTATGTTCCTGATTTTTAATATAGTATATATGTTACCAGTAGCCTATGTACATTTTTTTGGGTTCTCCCTTGGAGGGGTTGAAGAGATTCTCAACGGTGATCCCAGTATGCTTGCAGATATGATGGTCTTTTACGTCGCTGTCTGGTTCTTTTATCTTGCCGGTTCGGCATTATTAGGATTTGGTATAAAAAATAAAAATATACAATGGATTATAGCATTCGAACTTCCAATTATTGTAAAGATTTTATTCAGTTTAGTTTTATTTTTTATAGTACTATCAAAAGTATTGCTTTATCCTGAAGGGGTTTACTCATCTTATGCCTTTGATTCTGGCGCTATGGCAAGTCGTGTCTGGAATATCTCGATGGGATTATCAGAACTAGGTATAATAATTTTTACATTTTGTTTAGTTACAAAGAATATAAAGTTTGCAGTTGTTACCTTTCTTATAGTCTCATTAAATCTACTACATGGGACTAGAATATTTACATTGATATTACTTTTAATGATCATATTTTATATAATTTTTATTAATAAAAAAATATCAAAGCTGAAATTATTTATTATTTTGAGCCTTTTTTTTGGCGCAATAGTGATATCATTTTTGATAATATTCATTATCCGTTCTAATGTTTCAATTGAAAATATAAATATAGACCTAATTCTAAGTCCAATAGTATATGAGTCTTTATTTAATCAAATATCTTTTATGCGGATGCTGGATTGGCTACATCAAGGGGCAGTTCCGTTTGCACCACAAATGCTTTTTTCTGATTCAGCTATATTTACGTTACCGACTTTTCTTTTTGATGAAAAATCATCTTTAATGTATATAAATAAATTTGGAGAACTTAGCCCTTTAGGTGGGCTTTCCGGTTATGCTAGTGCAGTAATATATTTTTCGTATTATTATTTCCTGTGGTATTTTATTCTCGGTATTACATCAAGCTTATTATTAAGGTTTACATCGAGTGTAAACTTTGTAATATTGTCGAGAGTTAT\r\n+>O-9,46_wbaV\r\n+ATGAAGGTATCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGACCTTCTTGAAAGTATTAATAATCAATCTTCTCACTCCTTAATTGTAGAAGTATGTATTTCAGATAATGCATCAACTGATGGAACTGAAGAGTCAATAAATATCTGGAGAGATAGATTTAATTTTCCAATTTTGTATCAAAGGCATAACGAAAATATTGGGCCAGATAGGAATTATTTATCTGCAGTTAATATGGGGACTGGAGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAATTCCCTTGCATTGATGGAAGATAAATTGGCTGCCGGAAGTGGCATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAAAATATCTAATCCACATCGGCGATGGTTAAATGGTGGCAGTAGATTATTTTCTTTTAGCAATGAAGCTGATTTGATAGAGTACTTTAGTAAATGTAACTCAGTCGGCGGACTTTTTAGCTACTTAAGCTCTATTATAGTGAAAAGGAATAAATGGTCTGACGTCATATTTGACGAGTCATACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTGCAGTACATATCACTGCCACTGGTTGATTGCAGAGGAAATAACGATACATTCGAAAGTAATGGGAAGGCTCGTCGAATAAAAATTGATTTCATCGGTTATTTAAAACTGAGGGAGGATTTTTATAATAACAATACAAAAATATATATCTCATTTGGACGGGTTCTTACAAAAGAGCGTCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACCGATAGGGCTGAACTTGCATCATTTTATAAGAAGTTGGGATATCCGAAAATAGCCACCAATTTAATATTTCGTCTTAAAGGGCTGGCTAGCTACACTAAAAAAATAAAATTAGCAAAAATGGTAATAAAAAAAATATTTTCATAG\r\n+>O-9,46_wzy\r\n+ATGAGATGTGCTATGGTATTTTTAGCGTGGTTTATTGCTATTGGGATATATATAATATGTGGTATTTTTTATCTTCAATTTCCTCAATTATCACCACTAGGGGCTCTTGCATATACTGATACAGTGGGCGATGTAATCATTGTCGTATCCACGGGGATAGTGGGAGTTTTTCTCGGCTATTTTGCATTTTCTAAAATCAAGTTAGTAGGAATAAAAGATTTTAATAATTCGTGTTTTATAAATTTTTGTTCAGTATGCTTTATTATTTCAGCGTTTCTAATTTTCGCCTTAGGCGTCGCTGCATATGGTGGTTACATAGCATTTCTACATACGCCTTATATAGCAATCTATGAAGGTAGTGCAGAAAATCAAACCAGAGATATCCTCATATCTTCATCGGGATTGCTTGCTAACTATGCACTATTAACTAGCATTCGTGTCAACTTTAAAGAAATATCAATAACTAATAAAGTTGTCATAGCAGTATCGCTATTAATACTTGTTTCTATATTTATTCAGGGACGAAGAGAAAATTTAATTTTGCTAATATTATGTTTCGTGTCATTCTATATGCTAAATTATAAAATTAATTTTAAACGTATTATCAAAGTAAGCATTATTTGTATAATAATGTTTTTCATTGCTGGATTAGGTTTATATTTGCGTGAAAGCACTTCAACTTCAGGAGGAAGTATTTTTACAGCTATACCTTTTGCCGTGATGTATGAAACACATTTTTCTTTAGCGACTTTGGCTAATGAAGTGAGAACGCATTTATATAATAATTTACCTTATGGGGGAGTATTAGATTTATTTTCTCCCATATTATTTATTATCCCTGCTTTTATATATGGGATTTTTGGTTTAGATAAACAATCTTTGTTCGAGAATAATGAGATGCGTTTTTATGAGGATAAAGGCGGCCAGTTTATATTCACAGAGGCTTTTCATTCACTTGGTTATGTCGGAGTATTCCTGCATGGTTTAATCTTGGGTGTAATGCTAATAGTATTTTATCGTGTAGCCAAGAAAAGCAGGCTCATAATTTATCATTTTCCAATTATTTCCCTCATATTTGTTGCAATGAGAAAAGACCTTACCTATGGTGTTAAATATATTTCTCTTTTGTTCATATTTATGATGATTTTTTATTTCATCTATAAGTTACTCCCACTTAAAAATAATGGTTGA\r\n+>sdf-I_AF370707 \r\n+GATCTATCCTAATGAAAATAAATGTGTTTTATCTGATGCAAGAGGGGGAGGGAGGAGCTTTAGCCAAAAG\r\n+AAAACCGCCGGGAGAGGCGGTTTGATGTGGTTGGTTCGTCACTGATTTTTTAGGCGCTTTTGTGCAGCGA\r\n+GCATGTTCTGGAAAGCCTCTTTATATAGCTCATTCTGACCTCTAAGCCGGTCAATGAGTTTTTCTTTCTC\r\n+AGATTCAGGGAGTATATCAAAAAGGTTTAGTAAATCAGCCTGTTGTCTGCTCACCATTCGCCAGCCACCA\r\n+CCTTCGAAGTTGTCATCGTAAGTACCAGAAGAACGAACGTAGTTCATTAGATC\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/specific_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/specific_genes.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>sdf_I_AF370707 +GATCTATCCTAATGAAAATAAATGTGTTTTATCTGATGCAAGAGGGGGAGGGAGGAGCTTTAGCCAAAAG +AAAACCGCCGGGAGAGGCGGTTTGATGTGGTTGGTTCGTCACTGATTTTTTAGGCGCTTTTGTGCAGCGA +GCATGTTCTGGAAAGCCTCTTTATATAGCTCATTCTGACCTCTAAGCCGGTCAATGAGTTTTTCTTTCTC +AGATTCAGGGAGTATATCAAAAAGGTTTAGTAAATCAGCCTGTTGTCTGCTCACCATTCGCCAGCCACCA +CCTTCGAAGTTGTCATCGTAAGTACCAGAAGAACGAACGTAGTTCATTAGATC +>fliC_e,h_Salmonella.enterica_Newport_AY353379_e +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTTTCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTCTGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAATGGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATCCCGCGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACGAATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGCACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATGTTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGATAAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTACAGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGTCACAAAAACTGCGGCTAACCAACTTGGTGGCGTAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCGCAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACTTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Salmonella.enterica_Derby_AY353380_g,m +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTTTCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAGTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTGCTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTTGATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m_Salmonella.enterica_Enteritidis_AY353386_g,m +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTCCGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCTTCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGTGCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTCCGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACGGTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTGCAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAAATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTGCTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAAAATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCATTAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTTAATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA + + |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/database/tyr_of_O2_O9.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/database/tyr_of_O2_O9.fasta Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +> O-2_Salmonella enterica subsp. enterica serovar Paratyphi A str. JX05-19 contig01, whole genome shotgun sequence fliC region (_790377:790985_608bp) +ATGAAGCTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT +>O-9_Salmonella enterica subsp. enterica serovar Typhi str. E00-7866, contig contig00001, whole genome scathotgun sequence fliC region (_1410109:1410718_609bp) +ATGAAGCTTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/BWA_analysis_H_update_new_family_dependent.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/BWA_analysis_H_update_new_family_dependent.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,457 @@\n+#!/usr/bin/env python\r\n+\r\n+import os\r\n+from Bio import SeqIO\r\n+import sys\r\n+from Initial_functions import Uniq\r\n+from Bio.Blast import NCBIXML\r\n+\r\n+def BWA_analysis(sra_name,additional_file,database,mapping_mode,file_mode,z):\r\n+ global fliC_option\r\n+ global fljB_option\r\n+ global family_c_list\r\n+ global family_b_list\r\n+ global list_c_length\r\n+ global list_b_length\r\n+ family_c_list=[] #will catch families on the family test mapping\r\n+ family_b_list=[]\r\n+ if file_mode=="1":#interleaved\r\n+ if sra_name[-3:]=="sra":\r\n+ del_fastq=1\r\n+ for_fq=sra_name.replace(".sra","_1.fastq")\r\n+ rev_fq=sra_name.replace(".sra","_2.fastq")\r\n+ for_sai=sra_name.replace(".sra","_1.sai")\r\n+ rev_sai=sra_name.replace(".sra","_2.sai")\r\n+ sam=sra_name.replace(".sra",".sam")\r\n+ bam=sra_name.replace(".sra",".bam")\r\n+ else:\r\n+ del_fastq=0\r\n+ core_id=sra_name.split(".fastq")[0]\r\n+ for_fq=core_id+"-read1.fastq"\r\n+ rev_fq=core_id+"-read2.fastq"\r\n+ for_sai=core_id+"_1.sai"\r\n+ rev_sai=core_id+"_2.sai"\r\n+ sam=core_id+".sam"\r\n+ bam=core_id+".bam"\r\n+ elif file_mode=="2":#seperated\r\n+ forword_seq=sra_name\r\n+ reverse_seq=additional_file\r\n+ for_core_id=forword_seq.split(".fastq")[0]\r\n+ re_core_id=reverse_seq.split(".fastq")[0]\r\n+ for_fq=for_core_id+".fastq"\r\n+ rev_fq=re_core_id+".fastq"\r\n+ for_sai=for_core_id+".sai"\r\n+ rev_sai=re_core_id+".sai"\r\n+ sam=for_core_id+".sam"\r\n+ bam=sam.replace(".sam",".bam")\r\n+ elif file_mode=="3":#single-end\r\n+ if sra_name[-3:]=="sra":\r\n+ del_fastq=1\r\n+ for_fq=sra_name.replace(".sra","_1.fastq")\r\n+ rev_fq=sra_name.replace(".sra","_2.fastq")\r\n+ for_sai=sra_name.replace(".sra","_1.sai")\r\n+ rev_sai=sra_name.replace(".sra","_2.sai")\r\n+ sam=sra_name.replace(".sra",".sam")\r\n+ bam=sra_name.replace(".sra",".bam")\r\n+ else:\r\n+ del_fastq=0\r\n+ core_id=sra_name.split(".fastq")[0]\r\n+ for_fq=core_id+".fastq"\r\n+ rev_fq=core_id+".fastq"\r\n+ for_sai=core_id+"_1.sai"\r\n+ rev_sai=core_id+"_2.sai"\r\n+ sam=core_id+".sam"\r\n+ bam=core_id+".bam"\r\n+\r\n+ database=database.split("/")[-1]##########1/27/2015\r\n+ os.system("bwa index database/"+database)\r\n+ if file_mode!="3":\r\n+ if mapping_mode=="mem":\r\n+ os.system("bwa mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai)\r\n+ os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ else:\r\n+ if mapping_mode=="mem":\r\n+ os.system("bwa mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" > "+sam) \r\n+ os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)\r\n+ os.system("samtools view -h -o "+sam+" "+bam)\r\n+ file=open(sam,"r")\r\n+ handle=file.readlines()\r\n+ name_list=[]\r\n+ for line in handle:\r\n+ if len(line)>300:\r\n+ name_list.append(line.split("\\t")[2])\r\n+ a,b=Uniq(name_list)\r\n+ c=dict(zip(a,b))\r\n+ Sero_list_C=[]\r\n+ Sero_list_B=[]\r\n+ description=[] #for storage of whole desription to extract the multifasta file for second BWA mapping\r\n+ fliC={}\r\n+ fljB={}\r\n+ for x in c:\r\n+ if x[:4]=="fliC":\r\n+ fliC[x]=c[x]\r\n+ for x in c:\r\n+ if x[:4]=="fljB":\r\n+ fljB[x]=c[x]\r\n+ final_fliC=sorted(fliC.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple w'..b'tabase/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai)\r\n+ os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) \r\n+ else:\r\n+ if mapping_mode=="mem":\r\n+ os.system("bwa mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" > "+sam)\r\n+ \r\n+ os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)\r\n+ os.system("samtools view -h -o "+sam+" "+bam)\r\n+ os.system("cat "+sam+"|awk \'{if ($5>=0) {print $10}}\'>"+database+sam+"_seq.txt")\r\n+ os.system("cat "+sam+"|awk \'{if ($5>=0) {print $1}}\'>"+database+sam+"_title.txt")\r\n+ file1=open(database+sam+"_title.txt","r")\r\n+ file2=open(database+sam+"_seq.txt","r")\r\n+ file1=file1.readlines()\r\n+ file2=file2.readlines()\r\n+ file=open(database+"_"+sam+".fasta","w")\r\n+ for i in range(len(file1)):\r\n+ title=">"+file1[i]\r\n+ seq=file2[i]\r\n+ if len(seq)>=50 and len(title)>6:#generally, can be adjusted with different situations\r\n+ file.write(title)\r\n+ file.write(seq)\r\n+ file.close()\r\n+ os.system("mv "+database+"_"+sam+".fasta"+" database")######1/27/2015\r\n+ os.system(\'makeblastdb -in database/\'+database+"_"+sam+".fasta"+\' -out \'+sam+".fasta"+\'_db \'+\'-dbtype nucl >temp.txt\') #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015\r\n+ os.system("blastn -query database/"+database2+" -db "+sam+".fasta"+"_db -out "+database2+"_vs_"+sam+".xml -outfmt 5 >temp.txt")###1/27/2015\r\n+ handle=open(database2+"_vs_"+sam+".xml")\r\n+ handle=NCBIXML.parse(handle)\r\n+ handle=list(handle)\r\n+ List=[]\r\n+ List_score=[]\r\n+ for i in range(len(handle)):\r\n+ if len(handle[i].alignments)>0:\r\n+ List.append(handle[i].query)\r\n+ score=0\r\n+ for j in range(len(handle[i].alignments)):\r\n+ for z in range(len(handle[i].alignments[j].hsps)):\r\n+ score+=handle[i].alignments[j].hsps[z].bits\r\n+ List_score.append(score)\r\n+ temp=dict(zip(List,List_score))\r\n+ Final_list=sorted(temp.iteritems(), key=lambda d:d[1], reverse = True)\r\n+ family=database2.split("_")[2]\r\n+ try:\r\n+ Final_list[0][0].split("_")[1] # or it will always print "$$$Genome...."(next line)\r\n+ print "$$$Genome:",sra_name\r\n+ print "$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1]\r\n+ print Final_list\r\n+ except:\r\n+ if type=="fliC":\r\n+ print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option\r\n+ if type=="fljB":\r\n+ print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option\r\n+ os.system("rm "+database2+"_vs_"+sam+".xml")###01/28/2015\r\n+ os.system("rm "+database+sam+"_seq.txt")###01/28/2015\r\n+ os.system("rm "+database+sam+"_title.txt")###01/28/2015\r\n+ os.system("rm temp.txt")###01/28/2015\r\n+ os.system("rm "+sam+".fasta"+"_db.*")###01/28/2015\r\n+\r\n+z=0\r\n+target=sys.argv[1] #should be sra format\r\n+data_base=sys.argv[2]\r\n+mapping_mode=sys.argv[3]\r\n+if sys.argv[4] not in ("1","2","3"):\r\n+ additional_file=sys.argv[4]\r\n+ file_mode=sys.argv[5]\r\n+else:\r\n+ additional_file=""\r\n+ file_mode=sys.argv[4]\r\n+BWA_analysis(target,additional_file,data_base,mapping_mode,file_mode,z)\r\n+\r\n+\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/BWA_analysis_O_new_dependent.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/BWA_analysis_O_new_dependent.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,280 @@\n+#!/usr/bin/env python\r\n+#tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2\r\n+\r\n+import os\r\n+from Bio import SeqIO\r\n+import sys\r\n+from Initial_functions import Uniq\r\n+from Bio.Blast import NCBIXML\r\n+\r\n+def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode):\r\n+ if file_mode=="1":#interleaved\r\n+ if sra_name[-3:]=="sra":\r\n+ os.system("fastq-dump --split-files "+sra_name)\r\n+ del_fastq=1\r\n+ for_fq=sra_name.replace(".sra","_1.fastq")\r\n+ rev_fq=sra_name.replace(".sra","_2.fastq")\r\n+ for_sai=sra_name.replace(".sra","_1.sai")\r\n+ rev_sai=sra_name.replace(".sra","_2.sai")\r\n+ sam=sra_name.replace(".sra",".sam")\r\n+ bam=sra_name.replace(".sra",".bam")\r\n+ else:\r\n+ del_fastq=0\r\n+ core_id=sra_name.split(".fastq")[0]\r\n+ try:\r\n+ os.system("gunzip "+sra_name)\r\n+ except:\r\n+ pass\r\n+ dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))\r\n+ os.system("perl "+dirpath+"/split_interleaved_fastq.pl --input "+core_id+".fastq --output "+core_id.replace(".","_")+".fastq")#######03152016\r\n+ ori_size=os.path.getsize(core_id+".fastq")#######03152016\r\n+ os.system("mv "+core_id.replace(".","_")+"-read1.fastq"+" "+core_id+"-read1.fastq")#######03152016\r\n+ os.system("mv "+core_id.replace(".","_")+"-read2.fastq"+" "+core_id+"-read2.fastq")#######03152016\r\n+ for_fq=core_id+"-read1.fastq"#######03152016\r\n+ rev_fq=core_id+"-read2.fastq"#######03152016\r\n+ if float(os.path.getsize(for_fq))/ori_size<=0.1 or float(os.path.getsize(rev_fq))/ori_size<=0.1:#09092015#12292015#######03152016\r\n+ os.system("echo haha")#09092015\r\n+ os.system("perl "+dirpath+"/splitPairedEndReads.pl "+core_id+".fastq")#09092015\r\n+ os.system("mv "+core_id+".fastq_1 "+for_fq)##09092015\r\n+ os.system("mv "+core_id+".fastq_2 "+rev_fq)##09092015\r\n+ else:#09092015\r\n+ os.system("echo hehe")#09092015\r\n+ for_sai=core_id+"_1.sai"\r\n+ rev_sai=core_id+"_2.sai"\r\n+ sam=core_id+".sam"\r\n+ bam=core_id+".bam"\r\n+ elif file_mode=="2":#seperated\r\n+ forword_seq=sra_name\r\n+ reverse_seq=additional_file\r\n+ try:\r\n+ os.system("gunzip "+forword_seq)\r\n+ except:\r\n+ pass\r\n+ try:\r\n+ os.system("gunzip "+reverse_seq)\r\n+ except:\r\n+ pass\r\n+ for_core_id=forword_seq.split(".fastq")[0]\r\n+ re_core_id=reverse_seq.split(".fastq")[0]\r\n+ for_fq=for_core_id+".fastq"\r\n+ rev_fq=re_core_id+".fastq"\r\n+ dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016\r\n+ print "check fastq id and make them in accordance with each other...please wait..."\r\n+ os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016\r\n+ for_sai=for_core_id+".sai"\r\n+ rev_sai=re_core_id+".sai"\r\n+ sam=for_core_id+".sam"\r\n+ bam=sam.replace(".sam",".bam")\r\n+ elif file_mode=="3":#single-end\r\n+ if sra_name[-3:]=="sra":\r\n+ os.system("fastq-dump --split-files "+sra_name)###01/28/2015\r\n+ del_fastq=1\r\n+ for_fq=sra_name.replace(".sra","_1.fastq")\r\n+ for_sai=sra_name.replace(".sra","_1.sai")\r\n+ sam=sra_name.replace(".sra",".sam")\r\n+ bam=sra_name.replace(".sra",".bam")\r\n+ else:\r\n+ del_fastq=0\r\n+ core_id=sra_name.split(".fastq")[0]\r\n+ try:\r\n+ os.system("gunzip "+sra_name)\r\n+ except:\r\n+ pass \r\n+ for_fq=core_id+".fastq"\r\n+ for_sai=core_id+"_1.sai"\r\n+ sam=core_id+".sam"\r\n+ bam=core_id+".bam"\r\n+ \r\n+ os.system("bwa index "+database)\r\n+ if file_mode!="3":\r\n+ if mapping_mode=="sam":\r\n+ os.system("bwa aln "+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa aln "+database+" "+rev_fq+" > "+rev_sai)\r\n+ os.system("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ elif mapping_mode=="mem":\r\n+ os.system("bwa mem "+database+" "+for_fq+"'..b'Most possilble Otype: O-1,3,19"\r\n+ else:\r\n+ try: \r\n+ O_choice=final_O[0][0].split("_")[0]\r\n+ if O_choice=="O-1,3,19":\r\n+ O_choice=final_O[1][0].split("_")[0]\r\n+ print "$$$Most possilble Otype: ",O_choice\r\n+ except:\r\n+ print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"\r\n+\r\n+\r\n+def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode):\r\n+ database="ParaA_rfb.fasta"\r\n+ os.system("bwa index database/"+database)###01/28/2015\r\n+ if rev_fq=="":#2015/09/09\r\n+ if mapping_mode=="mem":\r\n+ os.system("bwa mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":##\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" > "+sam)##\r\n+ else:\r\n+ if mapping_mode=="mem":\r\n+ os.system("bwa mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23\r\n+ elif mapping_mode=="sam":\r\n+ os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)\r\n+ os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai)\r\n+ os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ elif mapping_mode=="nanopore":\r\n+ os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" "+rev_fq+" > "+sam)\r\n+ os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)\r\n+ os.system("samtools view -h -o "+sam+" "+bam)\r\n+ os.system("cat "+sam+"|awk \'{if ($5>0) {print $10}}\'>"+sam+"_seq.txt")\r\n+ os.system("cat "+sam+"|awk \'{if ($5>0) {print $1}}\'>"+sam+"_title.txt")\r\n+ file1=open(sam+"_title.txt","r")\r\n+ file2=open(sam+"_seq.txt","r")\r\n+ file1=file1.readlines()\r\n+ file2=file2.readlines()\r\n+ file=open(sam+".fasta","w")\r\n+ for i in range(len(file1)):\r\n+ title=">"+file1[i]\r\n+ seq=file2[i]\r\n+ if len(seq)>=50 and len(title)>6:#generally,can be adjusted\r\n+ file.write(title)\r\n+ file.write(seq)\r\n+ file.close()\r\n+ database2="tyr_of_O2_O9.fasta"\r\n+ os.system(\'makeblastdb -in database/\'+database2+\' -out \'+database2+\'_db \'+\'-dbtype nucl\')\r\n+ os.system("blastn -query "+sam+".fasta"+" -db "+database2+"_db -out "+sam+"_vs_O29.xml -outfmt 5")\r\n+ handle=open(sam+"_vs_O29.xml")\r\n+ handle=NCBIXML.parse(handle)\r\n+ handle=list(handle)\r\n+ O9_bigger=0\r\n+ O2_bigger=0\r\n+ for x in handle:\r\n+ O9_score=0\r\n+ O2_score=0\r\n+ try:\r\n+ if \'O-9\' in x.alignments[0].hit_def:\r\n+ O9_score=x.alignments[0].hsps[0].bits\r\n+ O2_score=x.alignments[1].hsps[0].bits\r\n+ elif \'O-2\' in x.alignments[0].hit_def:\r\n+ O9_score=x.alignments[1].hsps[0].bits\r\n+ O2_score=x.alignments[0].hsps[0].bits\r\n+ if O9_score>O2_score:\r\n+ O9_bigger+=1\r\n+ if O9_score<O2_score:\r\n+ O2_bigger+=1\r\n+ except:\r\n+ continue\r\n+ print "$$$Genome:",sra_name\r\n+ if O9_bigger>O2_bigger:\r\n+ print "$$$Most possible Otype is O-9"\r\n+ elif O9_bigger<O2_bigger:\r\n+ print "$$$Most possible Otype is O-2"\r\n+ else:\r\n+ print "$$$No suitable one, because can\'t distinct it\'s O-9 or O-2, but ",potential_choice," has a more possibility."\r\n+ print "O-9 number is:",O9_bigger\r\n+ print "O-2 number is:",O2_bigger\r\n+\r\n+ os.system("rm "+sam+"_title.txt")###01/28/2015\r\n+ os.system("rm "+sam+"_seq.txt")###01/28/2015\r\n+ os.system("rm "+sam+".fasta")###01/28/2015\r\n+ os.system("rm "+database2+"_db.*")###01/28/2015\r\n+ os.system("rm "+sam+"_vs_O29.xml")###01/28/2015\r\n+\r\n+ \r\n+target=sys.argv[1] #should be sra format\r\n+data_base=sys.argv[2]\r\n+mapping_mode=sys.argv[3]\r\n+if sys.argv[4] not in ("1","2","3"):\r\n+ additional_file=sys.argv[4]\r\n+ file_mode=sys.argv[5]\r\n+else:\r\n+ additional_file=""\r\n+ file_mode=sys.argv[4]\r\n+\r\n+BWA_O_analysis(target,additional_file,data_base,mapping_mode,file_mode)\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/H_combination_output_analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/H_combination_output_analysis.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,296 @@\n+#!/usr/bin/env python\n+# "H_combination_output_analysis.py target.fasta fliCdatabase.fasta fljBdatabase.fasta"\n+# must have ispcr and primers of fliC and fljB at the same directory\n+\n+\n+import os\n+from Bio import SeqIO\n+import sys\n+from Bio.Blast import NCBIXML\n+from Initial_Conditions import phase1\n+from Initial_Conditions import phase2\n+\n+\n+\n+target=sys.argv[1]\n+database_fliC=sys.argv[2]\n+database_fljB=sys.argv[3]\n+output=target.split(\'.\')[0]+\'_out.fasta\'\n+\n+dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015\n+database_path="database"###01/27/2015,database_path=dirpath+"/database"\n+os.system(dirpath+\'/isPcr maxSize=3000 tileSize=7 minPerfect=7 minGood=7 \'+target+\' \'+dirpath+\'/../primers/seq_primer_fliC.txt \'+target+\'_fliC.fa\')\n+os.system(dirpath+\'/isPcr maxSize=3000 tileSize=7 minPerfect=7 minGood=7 \'+target+\' \'+dirpath+\'/../primers/seq_primer_fljB.txt \'+target+\'_fljB.fa\')\n+fliC=target+\'_fliC.fa\'\n+fljB=target+\'_fljB.fa\'\n+\n+if os.path.getsize(fliC)>10:\n+ os.system(\'makeblastdb -in \'+database_fliC+\' -out \'+database_fliC+\'_db \'+\'-dbtype prot\')###01/28/2015,no need to add fljB address, because input is abs address already\n+ os.system(\'blastx -seg=no -query \'+fliC+\' -db \'+database_fliC+\'_db \'+\'-out \'+\'FliC_Htype_\'+target+\'.xml \'+\'-outfmt 5\')\n+ print target\n+ fliC_XML=\'FliC_Htype_\'+target+\'.xml\'\n+ fliC_handle=open(fliC_XML)\n+ records=NCBIXML.parse(fliC_handle)\n+ fliC_records=list(records)\n+ E_thresh=1e-10\n+ hspbit=[]\n+ alignmentlist=[]\n+ for record in fliC_records:\n+ for alignment in record.alignments:\n+ hsp_bit_score=0\n+ startlist=[]#the percentage algorithm don\'t consider one situation, the new hsp cover old hsp\n+ endlist=[]#\n+ for hsp in alignment.hsps:\n+ start=hsp.query_start#\n+ end=hsp.query_end#\n+ leng=abs(start-end)#\n+ if hsp.expect<E_thresh:#\n+ if start>end:#\n+ temp=start#\n+ start=end#\n+ end=start#\n+ if len(startlist)==0:#\n+ hsp_bit_score=hsp_bit_score+hsp.bits#\n+ startlist.append(start)#\n+ endlist.append(end)#\n+ else:#\n+ for i in range(len(startlist)):#\n+ if startlist[i]<start<endlist[i]:#\n+ start=endlist[i]+1#\n+ if startlist[i]<end<endlist[i]:#03112016\n+ end=startlist[i]-1#\n+ if end<start:#the new hsp was included in old hsp#\n+ percentage=0#\n+ else:\n+ percentage=float(end-start)/leng#\n+ startlist.append(start)#\n+ endlist.append(end)#\n+ hsp_bit_score=hsp_bit_score+percentage*hsp.bits# \n+ alignment=alignment.hit_def+\':\'+str(hsp_bit_score)\n+ hspbit.append(hsp_bit_score)\n+ alignmentlist.append(alignment)\n+ scorelist=dict(zip(alignmentlist,hspbit))\n+ score=0\n+ serotype=[]\n+ seroscore=[]\n+ for Htype in scorelist:\n+ if scorelist[Htype]>score:\n+ First_Choice=Htype\n+ score=scorelist[Htype]\n+ if locals().has_key(\'First_Choice\'):\n+ serotype.append(First_Choice.split("__")[0])\n+ seroscore.append(score)\n+ secscore=0\n+ for Htype in scorelist:\n+\n+ if scorelist[Htype]>secscore and (Htype.split("__")[0] not in serotype):\n+ Sec_Choice=Htype\n+ secscore=scorelist[Htype]\n+ if locals().has_key(\'Sec_Choice\'): \n+ serotype.append(Sec_Choice.split("__")[0])\n+ seroscore.append(secscore)\n+ thirdscore=0\n+ for Htype in scorelist:\n+ if scorelist[Htype]>thirdscore and (Htype.split("__")[0] not in serotype):\n+ Third_Choice=Htype\n+ thirdscore=scorelist[Htype]\n+ if locals().has_key(\'Third_Choice\'):\n+ serotype.append(Third_Choice.split("__")[0])\n+ seroscore.append(thirdscore)\n+ print serotype,seroscore\n+ if score>100:\n+ print \'#\',target,\'$$$ Most possible H_fliC_type: \',First_Choice,\'\\n\'\n+ print \'$$$ bit_score:\',score,\'\\n\'\n+ if locals().has_key(\'secsco'..b' fljB_scorelist:\n+ if fljB_scorelist[Htype]>fljB_thirdscore and (Htype.split("__")[0] not in fljB_serotype):\n+ fljB_Third_Choice=Htype\n+ fljB_thirdscore=fljB_scorelist[Htype]\n+ if locals().has_key(\'fljB_Third_Choice\'):\n+ fljB_serotype.append(fljB_Third_Choice.split("__")[0])\n+ fljB_seroscore.append(fljB_thirdscore)\n+\n+ if fljB_score>100:\n+ print \'#\',target,\'$$$ Most possible H_fljB_type: \',fljB_First_Choice,\'\\n\'\n+ print \'$$$ Most bit_score:\',fljB_score,\'\\n\'\n+ if locals().has_key(\'fljB_secscore\'):\n+ if fljB_secscore>100:\n+ print \'#\',target,\'$$$ Second possible H_fljB_type: \',fljB_Sec_Choice,\'\\n\'\n+ print \'$$$ Second bit_score:\',fljB_secscore,\'\\n\'\n+ if locals().has_key(\'fljB_thirdscore\'):\n+ if fljB_thirdscore>100:\n+ print \'#\',target,\'$$$ Third possible H_fljB_type: \',fljB_Third_Choice,\'\\n\'\n+ print \'$$$ Third bit_score:\',fljB_thirdscore,\'\\n\'\n+ else:\n+ print \'$$$ No fljB in\',target\n+else:\n+ fljB_score=1\n+ print \'$$$ No fljB (no file created) in\',target\n+\n+\n+if score>100 and fljB_score>100:\n+ fliC_sero=dict(zip(serotype,seroscore))\n+ fljB_sero=dict(zip(fljB_serotype,fljB_seroscore))\n+ combination=[]\n+ combination_score=[]\n+ for seroname in fliC_sero:\n+ for fljB_seroname in fljB_sero:\n+ for i in range(len(phase1)):\n+ if phase1[i]==seroname and phase2[i]==fljB_seroname:\n+ name=seroname+"_"+fljB_seroname\n+ score=fliC_sero[seroname]+fljB_sero[fljB_seroname]\n+ combination.append(name)\n+ combination_score.append(score)\n+ combinationlist=dict(zip(combination,combination_score)) #we can do the filteration here\n+ final_dict=sorted(combinationlist.iteritems(), key=lambda d:d[1], reverse = True)\n+ print "$$_H:Order:",final_dict\n+elif score>100 and fljB_score<100:\n+ print "$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice\n+elif score<100 and fljB_score>100:\n+ print "$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice\n+elif score==1 and fljB_score>100:\n+ print "$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice\n+elif score==1 and fljB_score<100:\n+ print "$$_H:No fliC (file) existed, and no fljB"\n+elif score>100 and fljB_score==1:\n+ print "$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice\n+elif score<100 and fljB_score==1:\n+ print "$$_H:No fljB (file) existed, and no fliC"\n+else:\n+ print "$$_H:No fliC and fljB"\n+\n+\n+\'\'\'\n+E_thresh=1e-10\n+hspbit=[]\n+alignmentlist=[]\n+for record in fliC_records:\n+ for alignment in record.alignments:\n+ hsp_bit_score=0\n+ for hsp in alignment.hsps:\n+ if hsp.expect<E_thresh:\n+ hsp_bit_score=hsp_bit_score+hsp.bits\n+ alignment=alignment.hit_def+\':\'+str(hsp_bit_score)\n+ hspbit.append(hsp_bit_score)\n+ alignmentlist.append(alignment)\n+\n+scorelist=dict(zip(alignmentlist,hspbit))\n+score=0\n+for Htype in scorelist:\n+ if scorelist[Htype]>score:\n+ First_Choice=Htype\n+ score=scorelist[Htype]\n+if score>100:\n+ print \'#\',target,\'Most possible H_fliC_type: \',First_Choice,\'\\n\'\n+ print \'#bit_score:\',score,\'\\n\'\n+else:\n+ print \'#No fliC in\',target\n+\n+\n+E_thresh=1e-10\n+hspbit=[]\n+alignmentlist=[]\n+for record in fljB_records:\n+ for alignment in record.alignments:\n+ hsp_bit_score=0\n+ for hsp in alignment.hsps:\n+ if hsp.expect<E_thresh:\n+ hsp_bit_score=hsp_bit_score+hsp.bits\n+ alignment=alignment.hit_def+\':\'+str(hsp_bit_score)\n+ hspbit.append(hsp_bit_score)\n+ alignmentlist.append(alignment)\n+\n+scorelist=dict(zip(alignmentlist,hspbit))\n+fljB_score=0\n+for Htype in scorelist:\n+ if scorelist[Htype]>fljB_score:\n+ First_Choice=Htype\n+ fljB_score=scorelist[Htype]\n+if fljB_score>100:\n+ print \'#\',target,\'Most possible H_fljB_type: \',First_Choice,\'\\n\'\n+ print \'#bit_score:\',fljB_score,\'\\n\'\n+else:\n+ print \'#No fljB in\',target\n+\'\'\'\n+\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/Initial_Conditions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/Initial_Conditions.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b"@@ -0,0 +1,11 @@\n+#!/usr/bin/env python\n+\n+\n+\n+phase2=[u'1,7', u'e,n,x', u'1,6', u'1,7', u'1,6', u'1,6', u'1,6', u'-', u'1,6', u'1,6', u'1,5', u'1,5', u'z55', u'e,n,x,z15', u'z35', u'z', u'z53', u'z53', u'z54', u'-', u'z35', u'1,5,7', u'z', u'z', u'z53', u'z35', u'z35', u'z35', u'e,n,x,z15', u'z35', u'z35', u'z35', u'z53', u'z', u'z35', u'-', u'e,n,x', u'[e,n,x]', u'1,5,7', u'1,[5],7', u'e,n,x', u'1,2', u'e,n,z15', u'z6', u'z6', u'e,n,z15', u'z42', u'1,5', u'e,n,x', u'z39', u'z42', u'z6', u'l,v', u'1,5', u'e,n,x,z15', u'[1,5]', u'z10', u'1,5', u'l,z13,z28', u'1,7', u'e,n,x', u'e,n,z15', u'e,n,x', u'e,n,z15', u'1,5', u'1,7', u'1,7', u'1,2', u'e,n,z15', u'e,n,x', u'z6', u'1,6', u'1,5', u'1,6', u'e,n,z15', u'1,5', u'z42', u'e,n,z15', u'e,n,x', u'z39', u'1,5', u'1,5', u'z6', u'e,n,z15', u'e,n,x', u'z6', u'1,6', u'z6', u'1,7', u'1,2', u'1,6', u'z39', u'z6', u'1,5,7', u'1,5', u'1,7', u'z6', u'z39', u'1,7', u'-', u'e,n,x', u'e,n,z15', u'z39', u'e,n,x', u'1,2', u'-', u'e,n,z15', 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u'1,5', u'1,5', u'e,n,x', u'z42', u'z6', u'z6', u'1,5', u'[1,5]', u'z6', u'e,n,x', u'1,7', u'e,n,x', u'e,n,x', u'e,n,z15', u'1,6', u'l,w', u'1,7', u'e,n,z15', u'1,2', u'e,n,x', u'1,5', u'e,n,x', u'1,5', u'1,6', u'z39', u'e,n,z15', u'1,5', u'e,n,x,z15', u'1,6', u'z6', u'z35', u'z', u'e,n,x,z15', u'1,5', u'1,5', u'1,6', u'1,5', u'l,w', u'e,n,x,z15', u'1,5', u'z6', u'e,n,z15', u'1,5,7', u'1,2', u'1,7', u'1,7', u'1,6', u'e,n,x', u'z6', u'e,n,x', u'1,5', u'e,n,z15', u'1,6', u'-', u'1,5', u'1,7', u'e,n,x', u'1,5', u'e,n,x,z15', u'1,6', u'1,7', u'l,w', u'e,n,x', u'e,n,x', u'[e,n,z15]', u'z6', u'z6', u'1,2', u'1,5', u'e,n,x', u'1,6', u'1,5', u'1,6', u'1,7', u'k', u'e,n,x', u'e,n,z15', u'z6', u'e,n,z15', u'e,n,x', u'e,n,x', u'z6', u'e,n,z15', u'e,n,x', u'1,6', u'z39', u'z53', u'z', u'1,5,7', u'z6', u'l,w', u'e,n,z15', u'1,7', u'z35', u'1,5,7', u'1,6', u'1,5', u'1,2', u'z39', u'e,n,x,z15', u'1,5', u'1,6', u'1,7', u'z6', u'e,n,x', u'e,n,z15', u'l,w', u'z', u'e,n,x,z15', u'z6', u'1,6', u'1,5', u'e,n,z15', u'1,5', u'z6"..b"ogu', u'Planckendael', u'IIIa 59:z4,z23:-', u'IIIa 62:z4,z23:-', u'IIIa 63:z4,z23:-', u'Aequatoria', u'Yerba', u'Tabligbo', u'IV 43:z4,z23:-', u'Kua', u'Ploufragan', u'II 44:z4,z23:-', u'IIIa 44:z4,z23:-', u'IV 44:z4,z23:-', u'IV 50:z4,z23:-', u'IV 45:z4,z23:-', u'IIIa 41:z4,z23:-', u'Fehrbellin', u'Bere', u'Binche', u'IIIa 47:z4,z23:-', u'IIIa 48:z4,z23:-', u'IV 48:z4,z23:-', u'IIIa 45:z4,z23:-', u'IV 16:z4,z23:-', u'IV 6,14:z4,z23:-', u'Ilugun', u'Remete', u'Etterbeek', u'Wagadugu', u'Bellevue', u'IIIa 11:z4,z23:-', u'Bousso', u'Kibi', u'Axim', u'II 16:z4,z23:-', u'IV 11:z4,z23:-', u'Adabraka', u'Ekotedo', u'IIIa 13,22:z4,z23:-', u'Dabou', u'Ajiobo', u'Arapahoe', u'IIIa 17:z4,z23:-', u'Corvallis', u'Wangata', u'Ried', u'Lezennes', u'Chailey', u'IIIa 13,23:z4,z23,[z32]:-', u'IIIa 53:z4,z23,z32:-', u'IIIa 41:z4,z23,z32:-', u'IIIa 48:z4,z23,z32:-', u'IIIa 56:z4,z23,z32:-', u'IIIa 17:z4,z23,z32:-', u'IIIa 50:z4,z23,z32:-', u'IIIa 44:z4,z23,z32:-', u'IIIa 17:z4,z24:-', u'Christiansborg', u'Sambre', u'IV 43:z4,z24:-', u'Ipswich', u'Toricada', u'IIIa 41:z4,z24:-', u'Yehuda', u'IV [1],42:z4,z24:-', u'IIIa 42:z4,z24:-', u'IIIa 43:z4,z24:-', u'IIIb 48:z4,z24:-', u'Albany', u'Duesseldorf', u'IIIa 53:z4,z24:-', u'II 53:z4,z24:-', u'Natal', u'IIIa 51:z4,z24:-', u'IV 50:z4,z24:-', u'IIIa 50:z4,z24:-', u'II 9,46:z4,z24:z39', u'II 1,9,12,46,27:z4,z24:1,5', u'II 6,7:z4,z24:z42', u'IV 44:z4,z24:-', u'IIIa 48:z4,z24:-', u'Djakarta', u'Tamberma', u'Florian', u'II 3,10:z4,z24:-', u'IIIa 45:z4,z24:-', u'Transvaal', u'Somone', u'IV 6,7:z4,z24:-', u'Ngaparou', u'IV 16:z4,z24:-', u'Uzaramo', u'Chichiri', u'II 40:z4,z24:z39', u'Bangkok', u'IIIa 40:z4,z24:-', u'IIIa 35:z4,z24:-', u'IV [1],40:z4,z24:-', u'Westphalia', u'Kalamu', u'IIIa 44:z4,z24:-', u'Bodjonegoro', u'Kethiabarny', u'II 16:z4,z24:-', u'II 18:z4,z24:-', u'Romanby', u'IIIa 13,23:z4,z24:-', u'IIIa 21:z4,z24:-', u'II 21:z4,z24:-', u'Blukwa', u'Kaevlinge', u'IIIa 17:z4,z32:-', u'IIIa 45:z4,z32:-', u'IIIa 63:z4,z32:-', u'IIIa 62:z4,z32:-', u'IIIa 35:z4,z32:-', u'IIIa 18:z4,z32:-', u'IV 21:z4,z32:-', u'IV 48:z4,z32:-', u'IV 16:z4,z32:-', u'IV [1],44:z4,z32:-', u'IIIa 51:z4,z32:-', u'IIIa 48:z4,z32:-', u'IIIa 50:z4,z32:-', u'IV 50:z4,z32:-', u'Tallahassee', u'IV [1],40:z4,z32:-', u'IIIa 44:z4,z32:-', u'IV 43:z4,z32:-', u'IV 11:z4,z32:-', u'IIIa 41:z4,z32:-', u'IIIa 40:z4,z32:-', u'60:z41:-', u'Thayngen', u'Karamoja', u'Wuppertal', u'Hillsborough', u'Maska', u'Diogoye', u'Maastricht', u'VI 6,7:z41:1,7', u'Ottawa', u'Taset', u'48:z41:-', u'66:z41:-', u'Tamilnadu', u'Dortmund', u'II 50:z42:1,7', u'II 57:z42:1,6', u'II 1,6,14:z42:1,6', u'II 16:z42:1,(5),7', u'II 43:z42:[1,5,7]', u'II [1],9,12:z42:1,[5],7', u'II [1],40:z42:1,6', u'II 6,7:z42:1,[5],7', u'II 16:z42:1,6', u'Quinhon', u'Bulovka', u'II 52:z44:1,5,7', u'IIIb 58:z52:z35', u'IIIb 53:z52:z35', u'IIIb 53:z52:z53', u'IIIb 65:z52:z53', u'IIIb 65:z52:z35', u'IIIb 65:z52:z', u'IIIb 59:z52:z53', u'IIIb 58:z52:z', u'IIIb 61:z52:1,5,7', u'IV 41:z52:-', u'IIIb 16:z52:z35', u'IIIb 61:z52:z53', u'IIIb 61:z52:z35', u'IIIb 60:z52:1,5,[7]', u'IIIb 61:z52:z', u'IIIb 60:z52:z', u'IIIb 60:z52:z35', u'IIIb 60:z52:z53', u'IIIb 65:z52:e,n,x,z15', u'IIIb 47:z52:1,5', u'IIIb 48:z52:e,n,x,z15', u'IIIb 35:z52:1,5,7', u'IIIb 50:z52:z53', u'IIIb 47:z52:z35', u'IIIb 47:z52:z', u'IIIb 48:z52:z', u'IIIb 47:z52:1,5,7', u'IIIb 43:z52:z53', u'IIIb 35:z52:z', u'IIIb 35:z52:z35', u'IIIb [1],6,14,[25]:z52:z35', u'IIIb 6,14:z52:e,n,x,z15', u'IIIb 38:z52:z35', u'IIIb 38:z52:z53', u'IIIb 47:z52:e,n,x,z15', u'IIIb 42:z52:z', u'IIIb 50:z52:z35', u'IIIb 35:z52:e,n,x,z15', u'IIIb 50:z52:1,5,7', u'IIIb 38:z53:-', u'IIIb 47:z53:-', u'IIIb 42:z57:1,5', u'II 58:z6:1,6', u'II 30:z6:1,6', u'Franken', u'II 47:z6:1,6', u'II 16:z6:1,6', u'II 42:z6:1,6', u'II [1],40:z6:1,5', u'II 6,7:z6:1,7', u'Aesch', u'IIIb 38:z61:[z53]', u'48:z65:-', u'IIIb 21:z65:e,n,x,z15', u'66:z65:-', u'Pietersburg', u'Delmenhorst', u'48:z81:-', u'[1],40:z81:-', u'66:z81:-', u'II [1],40:z81:z6', u'Mygdal',u'Lubbock']\n" |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/Initial_Conditions.pyc |
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| Binary file SeqSero/libs/Initial_Conditions.pyc has changed |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/Initial_functions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/Initial_functions.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,42 @@ +#!/usr/bin/env python + + +def To_list(L): + import string + New_list=[] + for x in L: + x1=x[:-1] + x1=string.atoi(x1) + New_list.append(x1) + return New_list + + +def Uniq(L): #return the uniq list and the count number + Old=L + L.sort() + L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] + count=[] + for j in range(len(L)): + y=0 + for x in Old: + if L[j]==x: + y+=1 + count.append(y) + return (L,count) + + +def Parse_seros_in_genome_trakr(L): #return the sero names in the sra_result.xlsx, the next step is usually "Uniq" in above + names2=[] + for x in L: + if "serovar" in x: + key_word=x.split("serovar")[1].split("_")[1] #the seronames + if key_word!="str." and key_word!="group": #to eliminate some "serovar_str." and "serovar_group" + if key_word in ["I","II","III","IIIa","IIIb","IV","VI","B"]: #the serovar is behind those letters + if x.split("serovar")[1].split("_")[2]!="str.": + names2.append(x.split("serovar")[1].split("_")[2]) + else: + names2.append(x.split("serovar")[1].split("_")[1]) + return names2 + + + |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/Initial_functions.pyc |
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| Binary file SeqSero/libs/Initial_functions.pyc has changed |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/Otype_determine_analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/Otype_determine_analysis.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,779 @@\n+#!/usr/bin/env python\r\n+\r\n+\'\'\'\r\n+revised at 11/24/2013\r\n+note:\r\n+The .py file mainly designed to deal with 5 different situations: 1.the gnd and galF on same contig; 2.the two genes on different contigs;\r\n+3.the two genes on different contigs, and gnd gene is splitted by two contigs; 4.the two genes on different contigs, and galF gene is splitted by two contigs;\r\n+5.the two genes on different contigs, and the two genes are both splitted by two contigs respectively;\r\n+\r\n+input:\r\n+1) <gnd_galF_sequence>: a fasta file containing galF and gnd sequences\r\n+2) <target>: a fasta file containing the genome (may be seperated contigs), mainly as the blast database for <gnd_galF_sequence> to extract rfb region\r\n+3) <database>: a fasta file containing rfb regions of 46 different O-serotypes\r\n+\r\n+output: the region between the galF and gnd in the target(blatdb) sequebce (the rfb region, assuming the rfb region is flanked by the two genes)\r\n+synopsis: ./Otype_determine_analysis.py <gnd_galF_sequence> <target> <database>\r\n+\'\'\'\r\n+from __future__ import division\r\n+import sys\r\n+import os\r\n+from Bio.Blast import NCBIXML\r\n+from Bio import SeqIO\r\n+\r\n+\r\n+def test_O29(subdatabase):\r\n+ first_hspbit=[]\r\n+ first_alignmentlist=[]\r\n+ global Choice,Choice_score,O_9_score,O_2_score\r\n+ O_9_score=0\r\n+ O_2_score=0\r\n+ os.system(\'makeblastdb -in database/\'+subdatabase+\' -out \'+subdatabase+\'_db -dbtype nucl\')###01/28/2015\r\n+ os.system(\'blastn -query \'+target+\' -db \'+subdatabase+\'_db -out \'+subdatabase+\'_vs_\'+target+\'.xml \'+\'-outfmt 5\')###01/28/2015\r\n+ xml_file=subdatabase+\'_vs_\'+target+\'.xml\'\r\n+ result_handle=open(xml_file)\r\n+ blast_record=NCBIXML.parse(result_handle)\r\n+ records=list(blast_record)\r\n+ if subdatabase=="tyr_of_O2_O9.fasta":\r\n+ for record in records: #there are many records (i.e. the \'>\' in query file), so change another method\r\n+ for alignment in record.alignments:\r\n+ if \'O-9\' in alignment.hit_def:\r\n+ for hsp in alignment.hsps:\r\n+ if hsp.expect<E_thresh:\r\n+ O_9_score=O_9_score+hsp.bits\r\n+ elif \'O-2\' in alignment.hit_def:\r\n+ for hsp in alignment.hsps:\r\n+ if hsp.expect<E_thresh:\r\n+ O_2_score=O_2_score+hsp.bits\r\n+ if O_9_score>100:\r\n+ if O_9_score>O_2_score:\r\n+ print \'$$$ Most possible O_type: O-9\',\'\\n\'\r\n+ print \'$$$ longest_bit_score:\',O_9_score,\'\\n\'\r\n+ else:\r\n+ print \'$$$ Most possible O_type: O-2\',\'\\n\'\r\n+ print \'$$$ longest_bit_score:\',O_2_score,\'\\n\'\r\n+ else:\r\n+ print "Assumpition wrong, no O2 or O9, return to re-analysis"\r\n+ if (\'O-2_\' not in Sec_Choice) and (\'O-9_\' not in Sec_Choice):\r\n+ print \'$$$ Most possible O_type Choice (no tyr difference):\',Sec_Choice\r\n+ if ((\'O-2_\' in Sec_Choice) or (\'O-9_\' in Sec_Choice)) and (\'O-2_\' not in Third_Choice) and (\'O-9_\' not in Third_Choice):\r\n+ print \'$$$ Most possible O_type Choice (no tyr difference):\',Third_Choice\r\n+ os.system("rm tyr_of_O2_O9.fasta_db.*")###01/28/2015\r\n+ os.system("rm "+xml_file)###01/28/2015\r\n+ if subdatabase=="oafA_of_O4_O5.fasta":\r\n+ try:\r\n+ for record in records: #there are many records (i.e. the \'>\' in query file), so change another method\r\n+ for alignment in record.alignments:\r\n+ if \'O-4_full\' in alignment.hit_def:\r\n+ for hsp in alignment.hsps:\r\n+ if hsp.expect<E_thresh:\r\n+ O_9_score=O_9_score+hsp.bits\r\n+ elif \'O-4_5-\' in alignment.hit_def:\r\n+ for hsp in alignment.hsps:\r\n+ if hsp.expect<E_thresh:\r\n+ O_2_score=O_2_score+hsp.bits\r\n+ if O_9_score>100:\r\n+ if O_9_score>O_2_score:\r\n+ print \'$$$O5_none_7_base_deletion\',\'\\n\'\r\n+ print \'$$$ longest_bit_score:\',O_9_score,\'\\n\'\r\n+ else:\r\n+ print \'$$$O5-\',\'\\n\'\r\n+ print \'$$$ longest_bit_score:\',O_2_score,\'\\n\'\r\n+ else:\r\n+ print \'$$$O5_none_7_base_deletion,unsure\',\'\\n\'\r\n'..b"n==alignment.hit_def and len(alignment.hsps[0].sbjct)!=len(contig.seq):\r\n+ hitstart=alignment.hsps[0].sbjct_start\r\n+ hitend=alignment.hsps[0].sbjct_end\r\n+ if hitstart>hitend:\r\n+ buffer=hitstart\r\n+ hitstart=hitend\r\n+ hitend=buffer\r\n+ potential1=contig.seq[0:hitstart-1].tostring()\r\n+ title1='>'+target.split('.')[0]+' potential rfb region:'+alignment.hit_def+':0 to '+str(hitstart-1)+'_total:'+str(len(potential1))+'bp'\r\n+ potential2=contig.seq[hitend+1:].tostring()\r\n+ title2='>'+target.split('.')[0]+' potential rfb region:'+alignment.hit_def+':'+str(hitend+1)+' to contig end'+'_total:'+str(len(potential2))+'bp'\r\n+ aim_sequence=potential1\r\n+ title=title1\r\n+ if len(potential1)<len(potential2):\r\n+ aim_sequence=potential2\r\n+ title=title2\r\n+ outfile.write(title)\r\n+ outfile.write('\\n')\r\n+ outfile.write(aim_sequence)\r\n+ outfile.write('\\n')\r\n+\r\n+ \r\n+ for alignment in blast_record[1].alignments:\r\n+ for contig in target_seq:\r\n+ if contig.description==alignment.hit_def and len(alignment.hsps[0].sbjct)!=len(contig.seq):\r\n+ hitstart=alignment.hsps[0].sbjct_start\r\n+ hitend=alignment.hsps[0].sbjct_end\r\n+ if hitstart>hitend:\r\n+ buffer=hitstart\r\n+ hitstart=hitend\r\n+ hitend=buffer\r\n+ potential1=contig.seq[0:hitstart-1].tostring()\r\n+ title1='>'+target.split('.')[0]+' potential rfb region:'+alignment.hit_def+':0 to '+str(hitstart-1)+'_total:'+str(len(potential1))+'bp'\r\n+ potential2=contig.seq[hitend+1:].tostring()\r\n+ title2='>'+target.split('.')[0]+' potential rfb region:'+alignment.hit_def+':'+str(hitend+1)+' to contig end'+'_total:'+str(len(potential2))+'bp'\r\n+ aim_sequence=potential1\r\n+ title=title1\r\n+ if len(potential1)<len(potential2):\r\n+ aim_sequence=potential2\r\n+ title=title2\r\n+ outfile.write(title)\r\n+ outfile.write('\\n')\r\n+ outfile.write(aim_sequence)\r\n+ outfile.write('\\n')\r\n+\r\n+ \r\n+ outfile.close()\r\n+\r\n+ os.system('makeblastdb -in '+database+' -out '+database+'_db '+'-dbtype nucl')\r\n+ os.system('blastn -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5')\r\n+ xml_file='Blast_Otype_'+target+'.xml'\r\n+ print '\\n'\r\n+ filehandle=open(xml_file)\r\n+ records=NCBIXML.parse(filehandle)\r\n+ records=list(records)\r\n+ realrecord1=records[0]\r\n+ if len(records[1].alignments)>len(records[0].alignments):\r\n+ realrecord1=records[1]\r\n+ realrecord2=records[2]\r\n+ if len(records[3].alignments)>len(records[2].alignments):\r\n+ realrecord2=records[3]\r\n+ title='>'+records[0].query.split(':')[0]+'_combined_potential_sequences'\r\n+ filecontent=SeqIO.parse(output,'fasta')\r\n+ filecontent=list(filecontent)\r\n+ \r\n+ for contig in filecontent:\r\n+ if contig.description==realrecord1.query:\r\n+ sequence=contig.seq.tostring()\r\n+\r\n+ for contig in filecontent:\r\n+ if contig.description==realrecord2.query:\r\n+ sequence=sequence+contig.seq.tostring()\r\n+ \r\n+\r\n+ outfile=open('combined_sequence.fasta','w')\r\n+ outfile.write(title)\r\n+ outfile.write('\\n')\r\n+ outfile.write(sequence)\r\n+ outfile.close()\r\n+ \r\n+ os.system('blastn -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5')\r\n+ xml_file='Combined_seq_blast_'+target+'.xml'\r\n+ print '\\n'\r\n+\r\n+\r\n+ filehandle=open(xml_file)\r\n+ records=NCBIXML.parse(filehandle)\r\n+ records=list(records)\r\n+ E_thresh=1e-10\r\n+ show_result()\r\n+\r\n+\r\n+\r\n+else:\r\n+ print '$$$ $$$ No O_type result, Attention: unusual number of hits, no hits for galF or gnd! Check blast output...'+'\\n'\r\n+\r\n+\r\n+os.system('rm '+target+'_db.'+'*')\r\n+\r\n+\r\n+\r\n+ \r\n" |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/compare_and_change_two_fastq_id.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/compare_and_change_two_fastq_id.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,27 @@ +#!/usr/bin/env python + +import os,sys +file1=sys.argv[1] +file2=sys.argv[2] + + +def compare_and_change_two_fastq_id(file1,file2): + a=os.popen("head "+file1).read().split("\n") + b=os.popen("head "+file2).read().split("\n") + for x in a: + if x.startswith("@"): + a_title=x.split(" ")[0] + for x in b: + if x.startswith("@"): + b_title=x.split(" ")[0] + if a_title==b_title: + pass + else: + print "changing the title of two seperated fastq files..." + print a_title,b_title + os.system("sed "+"-i 's/.1 / /g' "+file1) + print "finished file1" + os.system("sed "+"-i 's/.2 / /g' "+file2) + print "finished file2" + +compare_and_change_two_fastq_id(file1,file2) \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/deletion_compare.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/deletion_compare.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,135 @@ + +import os +from Bio import SeqIO +import sys +from Initial_functions import Uniq +from Bio.Blast import NCBIXML + + +target=sys.argv[1] #should be sra format +test_gene=sys.argv[2] +mapping_mode=sys.argv[3] +if sys.argv[4] not in ("1","2","3"): + additional_file=sys.argv[4] + file_mode=sys.argv[5] +else: + additional_file="" + file_mode=sys.argv[4] + + + + +def Copenhagen(sra_name,additional_file,mapping_mode,file_mode): + if file_mode=="1":#interleaved + if sra_name[-3:]=="sra": + del_fastq=1 + for_fq=sra_name.replace(".sra","_1.fastq") + rev_fq=sra_name.replace(".sra","_2.fastq") + for_sai=sra_name.replace(".sra","_1.sai") + rev_sai=sra_name.replace(".sra","_2.sai") + sam=sra_name.replace(".sra",".sam") + bam=sra_name.replace(".sra",".bam") + else: + del_fastq=0 + core_id=sra_name.split(".fastq")[0] + for_fq=core_id+"-read1.fastq" + rev_fq=core_id+"-read2.fastq" + for_sai=core_id+"_1.sai" + rev_sai=core_id+"_2.sai" + sam=core_id+".sam" + bam=core_id+".bam" + elif file_mode=="2":#seperated + forword_seq=sra_name + reverse_seq=additional_file + for_core_id=forword_seq.split(".fastq")[0] + re_core_id=reverse_seq.split(".fastq")[0] + for_fq=for_core_id+".fastq" + rev_fq=re_core_id+".fastq" + for_sai=for_core_id+".sai" + rev_sai=re_core_id+".sai" + sam=for_core_id+".sam" + bam=sam.replace(".sam",".bam") + elif file_mode=="3":#single-end + if sra_name[-3:]=="sra": + del_fastq=1 + for_fq=sra_name.replace(".sra","_1.fastq") + rev_fq=sra_name.replace(".sra","_2.fastq") + for_sai=sra_name.replace(".sra","_1.sai") + rev_sai=sra_name.replace(".sra","_2.sai") + sam=sra_name.replace(".sra",".sam") + bam=sra_name.replace(".sra",".bam") + else: + del_fastq=0 + core_id=sra_name.split(".fastq")[0] + for_fq=core_id+".fastq" + rev_fq=core_id+".fastq" + for_sai=core_id+"_1.sai" + rev_sai=core_id+"_2.sai" + sam=core_id+".sam" + bam=core_id+".bam" + + database="complete_oafA.fasta" + os.system("bwa index database/"+database)###01/28/2015 + if mapping_mode=="mem": + os.system("bwa mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23 + elif mapping_mode=="sam": + os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai) + os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai) + os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam) + os.system("samtools view -F 4 -Sbh "+sam+" > "+bam) + os.system("samtools view -h -o "+sam+" "+bam) + os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt") + os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt") + file1=open(sam+"_title.txt","r") + file2=open(sam+"_seq.txt","r") + file1=file1.readlines() + file2=file2.readlines() + file=open(sam+".fasta","w") + for i in range(len(file1)): + title=">"+file1[i] + seq=file2[i] + if len(seq)>40 and (len(title)>5 or ("@" not in title)): + file.write(title) + file.write(seq) + file.close() + database2="oafA_of_O4_O5.fasta" + os.system('makeblastdb -in database/'+database2+' -out '+database2+'_db '+'-dbtype nucl') + os.system("blastn -query "+sam+".fasta"+" -db "+database2+"_db -out "+sam+"_vs_O45.xml -outfmt 5") + handle=open(sam+"_vs_O45.xml") + handle=NCBIXML.parse(handle) + handle=list(handle) + O9_bigger=0 + O2_bigger=0 + for x in handle: + O9_score=0 + O2_score=0 + try: + if 'O-4_full' in x.alignments[0].hit_def: + O9_score=x.alignments[0].hsps[0].bits + O2_score=x.alignments[1].hsps[0].bits + elif 'O-4_5-' in x.alignments[0].hit_def: + O9_score=x.alignments[1].hsps[0].bits + O2_score=x.alignments[0].hsps[0].bits + if O9_score>O2_score: + O9_bigger+=1 + if O9_score<O2_score: + O2_bigger+=1 + except: + continue + print "$$$Genome:",sra_name + if O9_bigger>O2_bigger: + print "$$$Typhimurium" + elif O9_bigger<O2_bigger: + print "$$$Typhimurium_O5-" + else: + print "$$$Typhimurium, even no 7 bases difference" + print "O-4 number is:",O9_bigger + print "O-4_5- number is:",O2_bigger + os.system("rm "+sam+"_title.txt")###01/28/2015 + os.system("rm "+sam+"_seq.txt")###01/28/2015 + os.system("rm "+sam+".fasta")###01/28/2015 + os.system("rm "+database2+"_db.*")###01/28/2015 + os.system("rm "+sam+"_vs_O45.xml")###01/28/2015 + +if test_gene=="oafA": + Copenhagen(target,additional_file,mapping_mode,file_mode) \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/isPcr |
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| Binary file SeqSero/libs/isPcr has changed |
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| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/run_auto_All_for_assemblies.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/run_auto_All_for_assemblies.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,282 @@\n+#!/usr/bin/env python\r\n+\r\n+\r\n+\r\n+import os\r\n+from Bio import SeqIO\r\n+import sys\r\n+import itertools\r\n+from Initial_Conditions import phase1\r\n+from Initial_Conditions import phase2\r\n+from Initial_Conditions import phaseO\r\n+from Initial_Conditions import sero\r\n+import time\r\n+import multiprocessing\r\n+import string\r\n+\r\n+#m=string.atoi(sys.argv[1])\r\n+m=1 #temperorily, m can be set as one, because we just need one core to deal with it\r\n+file_name=sys.argv[1]\r\n+\r\n+def Combine(b,c):\r\n+ fliC_combinations=[]\r\n+ fliC_combinations.append(",".join(c))\r\n+ temp_combinations=[]\r\n+ for i in range(len(b)):\r\n+ for x in itertools.combinations(b,i+1):\r\n+ temp_combinations.append(",".join(x))\r\n+ for x in temp_combinations:\r\n+ temp=[]\r\n+ for y in c:\r\n+ temp.append(y)\r\n+ temp.append(x)\r\n+ temp=",".join(temp)\r\n+ temp=temp.split(",")\r\n+ temp.sort()\r\n+ temp=",".join(temp)\r\n+ fliC_combinations.append(temp)\r\n+ return fliC_combinations\r\n+\r\n+\r\n+def Test(file1,z,q):\r\n+ fliC="?"\r\n+ fljB="?"\r\n+ Otype="?"\r\n+ oafA=""#$$$$\r\n+ O3_10=""\r\n+ O1_3_19=""\r\n+ file2=file1.replace(\' \',\'_\').replace(":","__").replace("[","").replace("]","")\r\n+ try:\r\n+ os.rename(file1, file2)\r\n+ real_file=file2\r\n+ except:\r\n+ real_file=file1\r\n+ #print "###The genome name:",file1\r\n+ dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015\r\n+ os.system(\'touch result.txt\')\r\n+ database_path="database"###01/27/2015\r\n+ os.system(\'python \'+dirpath+\'/Otype_determine_analysis.py \'+database_path+\'/Typhimurium_LT2_gnd_galF.fasta \'+real_file+\' \'+database_path+\'/new_Oserotype.fasta >temp_result_\'+str(q)+\'O.txt\')\r\n+ os.system(\'cat temp_result_\'+str(q)+\'O.txt>>data_log.txt\')\r\n+ handle=open(\'temp_result_\'+str(q)+\'O.txt\',"r")\r\n+ handle=handle.readlines()\r\n+ for line in handle:\r\n+ if "$$$ Most" in line and "O_type" in line:\r\n+ Otype=line.split("O-")[1].split("_")[0].split(" ")[0]\r\n+ Otype=Otype.replace("\\n","").strip()\r\n+ #print line,\r\n+ elif "$$$ No" in line:\r\n+ Otype="-"\r\n+ if "O-9" in line:\r\n+ Otype="9"\r\n+ #print line,\r\n+ elif "$$$O5-" in line:#$$$\r\n+ oafA="-"\r\n+ elif "$$$O3,10 more possible" in line:#$$$\r\n+ O3_10="+"\r\n+ elif "$$$O1,3,19 more possible" in line:\r\n+ O1_3_19="+"\r\n+ if Otype=="1,3,19" or Otype=="3,10":#$$$judge O3,10 before formula forms\r\n+ if O3_10=="+":\r\n+ Otype="3,10"\r\n+ elif O1_3_19=="+":\r\n+ Otype="1,3,19"\r\n+ else:\r\n+ print "No_O3,10_O1,3,19_spe_sequences"\r\n+ os.system(\'python \'+dirpath+\'/H_combination_output_analysis.py \'+real_file+\' \'+database_path+\'/H_new_fliC_protein_database.fasta \'+database_path+\'/H_new_fljB_protein_database.fasta >temp_result_\'+str(q)+\'H.txt\')\r\n+ os.system(\'cat temp_result_\'+str(q)+\'H.txt>>data_log.txt\')\r\n+ handle2=open(\'temp_result_\'+str(q)+\'H.txt\',"r")\r\n+ handle2=handle2.readlines()\r\n+ suspect="no" #for the first choice doesn\'t hit core sequence\r\n+ for line in handle2:\r\n+ if "$$$ Most" in line and "fliC" in line:\r\n+ #print line,\r\n+ fliC=line.split("fliC_type: ")[1].split("_")[0].strip()\r\n+ if fliC=="g,m,p,s":\r\n+ fliC="g,m,s"\r\n+ elif "$$$ No" in line and "fliC" in line:\r\n+ fliC="-"\r\n+ #print line,\r\n+ elif "$$$ Most" in line and "fljB" in line:\r\n+ #print line,\r\n+ fljB=line.split("fljB_type: ")[1].split("_")[0].strip()\r\n+ elif "$$$ No" in line and "fljB" in line:\r\n+ fljB="-"\r\n+ #print line,\r\n+ if Otype=="9" and fliC=="g,m" and fljB=="-":\r\n+ os.system(\'python \'+dirpath+\'/special_gene_test_assemblies.py \'+database_path+\'/specific_genes.fasta \'+real_file+\' sdf >temp_result_\'+str(q)+\'sdf.txt\')\r\n+ os.system(\'cat temp_result_\'+str(q)+\'sdf.txt>>data_log.txt\')\r\n+ handle3=open(\'temp_result_\'+str(q)+\'sdf.txt\',"r")\r\n+ sdf=""\r\n+ for line in handle3:\r\n+ if "$$$" in line and "got a hit" in line:\r\n+ #print line,\r\n+ sdf="+"\r\n+ if sdf!="+":\r\n+ sdf="-"\r\n+\r\n+ seroname'..b'ntiated by phenotypic profile or genetic criteria.\\n"##\r\n+ predict_sero="See comments below"#\r\n+ elif predict_form=="4:i:-":#03252016#\r\n+ predict_sero="potential monophasic variant of Typhimurium"#03252016#\r\n+ elif predict_form=="4:r:-":#03252016#\r\n+ predict_sero="potential monophasic variant of Heidelberg"#03252016# \r\n+ elif predict_form=="4:b:-":#03252016#\r\n+ predict_sero="potential monophasic variant of Paratyphi B"#03252016# \r\n+ elif predict_form=="8:e,h:1,2":#03282016#\r\n+ predict_sero="Newport"#03282016#\r\n+ star="*"##03282016#\r\n+ star_line="Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."#03282016#\r\n+ claim="The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes."##\r\n+ if "N/A" in predict_sero:###added after standalone version, 2015/2/3\r\n+ claim=""###added after standalone version, 2015/2/3 \r\n+ \'\'\'\r\n+ new_file=open(file2+".txt","w")\r\n+ new_file.write(file2+"\\t"+"O-"+Otype+"\\t"+fliC+"\\t"+fljB+"\\t"+Otype+":"+fliC+":"+fljB+"\\t"+(" or ").join(seronames)+"\\t"+answer+"\\t"+suspect+"\\n")\r\n+ new_file.close()\r\n+ \'\'\'\r\n+ if "Typhimurium" in predict_sero and oafA=="-":#$$$$#03252016#\r\n+ predict_sero=predict_sero.strip()+"(O5-)"#03252016#\r\n+ star="*"#\r\n+ star_line="Detected the deletion of O5-."\r\n+ new_file=open("Seqsero_result.txt","w")\r\n+ new_file.write("Input files:\\t"+file2+"\\n"+"O antigen prediction:\\t"+"O-"+Otype+"\\n"+"H1 antigen prediction(fliC):\\t"+fliC+"\\n"+"H2 antigen prediction(fljB):\\t"+fljB+"\\n"+"Predicted antigenic profile:\\t"+predict_form+"\\n"+"Predicted serotype(s):\\t"+predict_sero+star+"\\n"+star+star_line+claim+"\\n")##\r\n+ new_file.close()\r\n+ os.system("rm temp_result_"+str(q)+"*.txt")###01/28/2015\r\n+ os.system("rm result.txt")###01/28/2015\r\n+ #os.system("rm -rf database")###01/28/2015 \r\n+ os.system("rm *.fasta *.xml *.fa")###01/28/2015\r\n+\r\n+ \r\n+def main():\r\n+ files1=[]\r\n+ files1.append(file_name)\r\n+ file_names=[]\r\n+ fastq_names=[]\r\n+ for file1 in files1:\r\n+ if file1[-6:]==\'.fasta\' or file1[-4:]==\'.fna\' or file1[-3:]==\'.fa\' or file1[-4:]==\'.fsa\':\r\n+ file_names.append(file1)\r\n+ if file1[-9:]==".fastq.gz" or file1[-6:]==".fastq":\r\n+ core_name=file1[:8]\r\n+ fastq_names.append(core_name)\r\n+ fastq_names=list(set(fastq_names))\r\n+ file_names=file_names+fastq_names\r\n+ for i in range(0,len(file_names),m):\r\n+ jobs=[]\r\n+ txt_names=[]\r\n+ if len(file_names)>=i+m:\r\n+ for j in range(m):\r\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i],i+j+1,i+j,))\r\n+ jobs.append(p)\r\n+ p.start()\r\n+ else:\r\n+ t=m+i-len(file_names)\r\n+ for j in range(m-t):\r\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i],i+j+1,i+j,))\r\n+ jobs.append(p)\r\n+ p.start()\r\n+ \'\'\'\r\n+ for j in xrange(len(jobs)):\r\n+ jobs[j].join()\r\n+ txt_names.append(file_names[j+i].replace(\' \',\'_\').replace(":","__").replace("[","").replace("]","")+".txt")\r\n+ print txt_names\r\n+ for j in xrange(len(txt_names)):\r\n+ print i,"and",j\r\n+ print i+j+1\r\n+ file=open(txt_names[j],"r")\r\n+ handle=list(file)\r\n+ b=handle[0].split("\\t")\r\n+ print b\r\n+ sheet.write(i+j+1,0,b[0])\r\n+ sheet.write(i+j+1,1,b[1])\r\n+ sheet.write(i+j+1,2,b[2])\r\n+ sheet.write(i+j+1,3,b[3])\r\n+ sheet.write(i+j+1,4,b[4])\r\n+ sheet.write(i+j+1,5,b[5])\r\n+ sheet.write(i+j+1,6,b[6])\r\n+ sheet.write(i+j+1,7,b[7])\r\n+\r\n+ print "End time,",time.time()\r\n+ file3.save("Seqsero_result2.xls")\r\n+ \'\'\'\r\n+\r\n+\r\n+if __name__ == \'__main__\':\r\n+ main()\r\n+\r\n+\r\n+\r\n+\r\n+\r\n+\r\n+\r\n+\r\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/run_auto_All_for_web_multi_revise.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/run_auto_All_for_web_multi_revise.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| b'@@ -0,0 +1,315 @@\n+#!/usr/bin/env python\n+\n+\n+\n+import os\n+from Bio import SeqIO\n+import sys\n+import itertools\n+from Initial_Conditions import phase1\n+from Initial_Conditions import phase2\n+from Initial_Conditions import phaseO\n+from Initial_Conditions import sero\n+import time\n+import multiprocessing\n+import string\n+\n+#m=string.atoi(sys.argv[1])\n+m=1 #temperorily, m can be set as one, because we just need one core to deal with it\n+file_name=sys.argv[1]\n+mapping_mode=sys.argv[2]\n+if sys.argv[3] not in ("1","2","3"):\n+ additional_file=sys.argv[3]\n+ file_mode=sys.argv[4]\n+else:\n+ additional_file=""\n+ file_mode=sys.argv[3]\n+#mode=sys.argv[2]\n+\n+def Combine(b,c):\n+ fliC_combinations=[]\n+ fliC_combinations.append(",".join(c))\n+ temp_combinations=[]\n+ for i in range(len(b)):\n+ for x in itertools.combinations(b,i+1):\n+ temp_combinations.append(",".join(x))\n+ for x in temp_combinations:\n+ temp=[]\n+ for y in c:\n+ temp.append(y)\n+ temp.append(x)\n+ temp=",".join(temp)\n+ temp=temp.split(",")\n+ temp.sort()\n+ temp=",".join(temp)\n+ fliC_combinations.append(temp)\n+ return fliC_combinations\n+\n+\n+def Test(file1,additional_file,file_mode,mapping_mode,z,q):\n+ fliC="?"\n+ fljB="?"\n+ Otype="?"\n+ file2=file1.replace(\' \',\'_\').replace(":","__").replace("[","").replace("]","").replace(".fq",".fastq")\n+ thename=file2#$$$$$$\n+ try:\n+ os.rename(file1, file2)\n+ real_file=file2\n+ except:\n+ real_file=file1\n+ file2=additional_file.replace(\' \',\'_\').replace(":","__").replace("[","").replace("]","").replace(".fq",".fastq")\n+ try:\n+ os.rename(additional_file, file2)\n+ additional_file=file2\n+ except:\n+ pass\n+ #print "###The genome name:",file1\n+ dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015\n+ os.system(\'touch result.txt\')\n+ database_path="database"###01/27/2015, because we add one directory to the result directory\n+ if file_mode=="1":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_O_new_dependent.py \'+real_file+\' \'+database_path+\'/special_new_O_genes.fasta \'+mapping_mode+\' 1 >temp_result_\'+str(q)+\'O.txt\')###01/27/2015\n+ elif file_mode=="2":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_O_new_dependent.py \'+real_file+\' \'+database_path+\'/special_new_O_genes.fasta \'+mapping_mode+" "+additional_file+\' 2 >temp_result_\'+str(q)+\'O.txt\')###01/27/2015\n+ elif file_mode=="3":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_O_new_dependent.py \'+real_file+\' \'+database_path+\'/special_new_O_genes.fasta \'+mapping_mode+\' 3 >temp_result_\'+str(q)+\'O.txt\')###01/27/2015\n+ os.system(\'cat temp_result_\'+str(q)+\'O.txt>>data_log.txt\')###01/28/2015\n+ handle=open(\'temp_result_\'+str(q)+\'O.txt\',"r")\n+ handle=handle.readlines()\n+ sdf=""#\n+ for line in handle:\n+ if "$$$Most" in line:\n+ Otype=line.split("O-")[1].split(" ")[0]\n+ Otype=Otype.replace("\\n","").strip()\n+ #print line,\n+ elif "$$$No" in line:\n+ Otype="-"\n+ if "O-9" in line:\n+ Otype="9"\n+ #print line,\n+ if "$$$" in line and "got a hit" in line and "sdf" in line:#\n+ sdf="+"#\n+ if sdf!="+":#\n+ sdf="-"#\n+ if file_mode=="1":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_H_update_new_family_dependent.py \'+real_file+\' \'+database_path+\'/H_combine_update_9_03_2014_new.fasta \'+mapping_mode+\' 1 >temp_result_\'+str(q)+\'H.txt\')###01/27/2015\n+ if file_mode=="2":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_H_update_new_family_dependent.py \'+real_file+" "+database_path+\'/H_combine_update_9_03_2014_new.fasta \'+mapping_mode+\' \'+additional_file+\' 2 >temp_result_\'+str(q)+\'H.txt\')###01/27/2015\n+ if file_mode=="3":\n+ os.system(\'python \'+dirpath+\'/BWA_analysis_H_update_new_family_dependent.py \'+real_file+\' \'+database_path+\'/H_combine_update_9_03_2014_new.fasta \'+mapping_mode+\' 3 >temp_result_\'+str(q)+\'H.txt\')###01/27/2015\n+ os.system(\'cat temp_result_\'+str(q)+\'H.txt>>data_log.txt\')\n+ handle2=open(\'temp_result_\'+str(q)+\'H.txt\',"r")\n+ handle2=handle2.readlines()\n+ sus'..b'iC+":"+fljB+"\\t"+(" or ").join(seronames)+"\\t"+answer+"\\t"+suspect+"\\n")\n+ new_file.close()\n+ \'\'\'\n+ if "Typhimurium" in predict_sero or predict_form=="4:i:-":#03252016#\n+ if file_mode=="1":\n+ os.system(\'python \'+dirpath+\'/deletion_compare.py \'+real_file+\' oafA \'+mapping_mode+\' 1 >temp_result_\'+str(q)+\'Typhim.txt\')###02/06/2015\n+ if file_mode=="2":\n+ os.system(\'python \'+dirpath+\'/deletion_compare.py \'+real_file+\' oafA \'+mapping_mode+" "+additional_file+\' 2 >temp_result_\'+str(q)+\'Typhim.txt\')###02/06/2015\n+ if file_mode=="3":\n+ os.system(\'python \'+dirpath+\'/deletion_compare.py \'+real_file+\' oafA \'+mapping_mode+\' 3 >temp_result_\'+str(q)+\'Typhim.txt\')###02/06/2015\n+ os.system(\'cat temp_result_\'+str(q)+\'Typhim.txt>>data_log.txt\')###01/28/2015\n+ handle=open(\'temp_result_\'+str(q)+\'Typhim.txt\',"r")\n+ handle=handle.readlines()\n+ for line in handle:\n+ if "$$$Typhimurium_O5-" in line:\n+ predict_sero=predict_sero.strip()+"(O5-)"#03252016#\n+ star="*"#\n+ star_line="Detected the deletion of O5-."\n+ new_file=open("Seqsero_result.txt","w")\n+ new_file.write("Input files:\\t"+thename+" "+additional_file+"\\n"+"O antigen prediction:\\t"+"O-"+Otype+"\\n"+"H1 antigen prediction(fliC):\\t"+fliC+"\\n"+"H2 antigen prediction(fljB):\\t"+fljB+"\\n"+"Predicted antigenic profile:\\t"+predict_form+"\\n"+"Predicted serotype(s):\\t"+predict_sero+star+"\\n"+star+star_line+claim+"\\n")#+##\n+ new_file.close()\n+ os.system("rm temp_result_"+str(q)+"*.txt")###01/28/2015\n+ os.system("rm result.txt")###01/28/2015\n+ os.system("rm -rf database")###01/28/2015\n+ os.system("rm -f *.fq *.fastq *.sam *.bam *.sai *.sra")###02/07/2015\n+ #os.system("rm "+for_fq)###01/28/2015\n+ #os.system("rm "+rev_fq)###01/28/2015\n+ #os.system("rm "+for_sai)\n+ #os.system("rm "+rev_sai)\n+ #os.system("rm "+bam)\n+ #os.system("rm "+sam)###01/28/2015\n+ #os.system("rm temp.txt")###01/28/2015\n+ #os.system("rm "+sam+".fasta"+"_db.*")###01/28/2015\n+ #os.system("rm temp"+sra_name+".fasta")###01/28/2015 \n+\n+ \n+def main():\n+ file_pair=(file_name,additional_file)\n+ file_names=[]\n+ file_names.append(file_pair)\n+ for i in range(0,len(file_names),m):\n+ jobs=[]\n+ txt_names=[]\n+ if len(file_names)>=i+m:\n+ for j in range(m):\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i][0],file_names[j+i][1],file_mode,mapping_mode,i+j+1,i+j,))\n+ jobs.append(p)\n+ p.start()\n+ else:\n+ t=m+i-len(file_names)\n+ for j in range(m-t):\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i][0],file_names[j+i][1],file_mode,mapping_mode,i+j+1,i+j,))\n+ jobs.append(p)\n+ p.start()\n+\'\'\'\n+ files1=[]\n+ files1.append(file_name)\n+ file_names=[]\n+ fastq_names=[]\n+ for file1 in files1:\n+ if file1[-4:]==\'.sra\':\n+ file_names.append(file1)\n+ if file1[-9:]==".fastq.gz":#need to change\n+ fastq_names.append(file1)\n+ if file1[-6:]==".fastq":#need to change\n+ fastq_names.append(file1)\n+ fastq_names=list(set(fastq_names))\n+ file_names=file_names+fastq_names\n+ for i in range(0,len(file_names),m):\n+ jobs=[]\n+ txt_names=[]\n+ if len(file_names)>=i+m:\n+ for j in range(m):\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i],i+j+1,i+j,))\n+ jobs.append(p)\n+ p.start()\n+ else:\n+ t=m+i-len(file_names)\n+ for j in range(m-t):\n+ p = multiprocessing.Process(target=Test,args=(file_names[j+i],i+j+1,i+j,))\n+ jobs.append(p)\n+ p.start()\n+\'\'\'\n+\n+\'\'\'\n+ for j in xrange(len(jobs)):\n+ jobs[j].join()\n+ txt_names.append(file_names[j+i].replace(\' \',\'_\').replace(":","__").replace("[","").replace("]","")+".txt")\n+ print txt_names\n+ for j in xrange(len(txt_names)):\n+ print i,"and",j\n+ print i+j+1\n+ file=open(txt_names[j],"r")\n+ handle=list(file)\n+ b=handle[0].split("\\t")\n+ print b\n+\n+ print "End time,",time.time()\n+\'\'\'\n+\n+if __name__ == \'__main__\':\n+ main()\n' |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/special_gene_test_assemblies.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/special_gene_test_assemblies.py Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,63 @@ +#just an possible use, we can use it to replace H**.py, treat fliC and fljB as the target genes? + +from __future__ import division +import sys +import os +from Bio.Blast import NCBIXML +from Bio import SeqIO + +def special_gene(target_fie,database,gene_list): + database=database.split("/")[-1]##########1/27/2015 + os.system('makeblastdb -in database/'+database+' -out '+database+'_db -dbtype nucl')##########1/28/2015 + os.system('blastn -query '+target_file+' -db '+database+'_db -out '+database+'_vs_'+target_file+'.xml '+'-outfmt 5')##########1/28/2015 + xml_file=database+'_vs_'+target_file+'.xml' + result_handle=open(xml_file) + blast_record=NCBIXML.parse(result_handle) + records=list(blast_record) + E_thresh=1e-10 + for x in gene_list: + handle=SeqIO.parse("database/"+database,"fasta")##########1/28/2015 + length_list=[] + for y in handle: + if x in y.description: + length_x=len(y.seq) + length_list.append(length_x) + aver_len=float(sum(length_list))/len(length_list) + hspbit=[] + alignmentlist=[] + for record in records: + for alignment in record.alignments: + if x in alignment.hit_def: #multi gene database, so... + print x,"got a hit, evaluating the hit quality..." + score=0 + for hsp in alignment.hsps: + if hsp.expect<E_thresh: + score+=hsp.bits + alignment=alignment.hit_def+':'+str(score) + hspbit.append(score) + alignmentlist.append(alignment) + scorelist=dict(zip(alignmentlist,hspbit)) + score=0 + for Htype in scorelist: + if scorelist[Htype]>score: + First_Choice=Htype + score=scorelist[Htype] + if float(score)>=0.1*aver_len: + print "$$$",First_Choice,"got a hit, score:",score + else: + print "$$$No ",x,"exists" + os.system("rm "+database+"_db.*")##########1/28/2015 + os.system("rm "+xml_file)##########1/28/2015 + +database=sys.argv[1] +target_file=sys.argv[2] +gene_list=[] +a=1 +i=3 +while a==1: + try: + gene_list.append(sys.argv[i]) + i+=1 + except: + a=0 +special_gene(target_file,database,gene_list) \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/splitPairedEndReads.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/splitPairedEndReads.pl Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,21 @@ +use strict; +use warnings; +my $file = $ARGV[0]; +open(FILE, "<$file") || die "cannot open $file\n"; +open(OUT1, ">$file\_1") || die "cannot open $file\_1\n"; +open(OUT2, ">$file\_2") || die "cannot open $file\_2\n"; +while(<FILE>){ + chomp; + print OUT1 "$_\/1\n"; + print OUT2 "$_\/2\n"; + my $newline = <FILE>; chomp($newline); + print OUT1 substr($newline, 0, length($newline)/2)."\n"; + print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n"; + $newline = <FILE>; chomp($newline); + print OUT1 "$newline\/1\n"; + print OUT2 "$newline\/2\n"; + $newline = <FILE>; chomp($newline); + print OUT1 substr($newline, 0, length($newline)/2)."\n"; + print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n"; +} +close(FILE); |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/libs/split_interleaved_fastq.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/libs/split_interleaved_fastq.pl Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,317 @@ +#!/usr/bin/perl-w + +use strict; + +use warnings; + +use Getopt::Long; + +use Pod::Usage; + +use File::Basename; + +# Date: 14-05-2010 + +# This program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order. + +# Author: Ram Vinay Pandey + + + +# Define the variables + +my $input=""; + +my $output=""; + +my $help=0; + +my $test=0; + +my $verbose=1; + + + +my $usage="perl $0 --input interleaved_fastq_file.fastq --output output.fastq\n"; + + + +GetOptions( + + "input=s" =>\$input, + + "output=s" =>\$output, + + "test" =>\$test, + + "help" =>\$help + +) or pod2usage(-msg=>"Wrong options",-verbose=>1); + + + +pod2usage(-verbose=>2) if $help; + +Test::runTests() if $test; + + + +pod2usage(-msg=>"\n\tProvide an input file!!\n\n\t\t$usage\n\n",-verbose=>1) unless -e $input; + +pod2usage(-msg=>"\n\tProvide an output file!!\n\n\t\t$usage\n\n",-verbose=>1) unless $output; + + + + + +my ( $name, $path, $extension ) = File::Basename::fileparse ( $output, '\..*' ); + +my $output1 = $name."-read1.fastq"; + +my $output2 = $name."-read2.fastq"; + + + +open my $ofh1, ">$output1" or die "Could not open output file"; + +open my $ofh2, ">$output2" or die "Could not open output file"; + + + + + +open (IN, "<$input") or die ("Could not open file $input for reading\n"); + + + +while (<IN>) { + + chomp; + + s/\r/\n/g; + + # discard blank line + + if (m/^\s*$/g) { + + next; + + } + + else { + + # Reading all lines for read 1 + + if (m/^\s*\@.*1$/) { + + + + print $ofh1 "$_\n"; + + my $ct=0; + + while(my $l = <IN>) { + + + + $ct++; + + chomp $l; + + s/\r/\n/g; + + print $ofh1 "$l\n"; + + + + last if($ct ==3); + + + + } + + + + } + + # Reading all lines for read 2 + + if (m/^\s*\@.*2$/) { + + + + print $ofh2 "$_\n"; + + my $ct=0; + + while(my $l = <IN>) { + + + + $ct++; + + chomp $l; + + s/\r/\n/g; + + print $ofh2 "$l\n"; + + + + last if($ct ==3); + + } + + + + + + } + + + + } + +} + + + +close IN; + +close $ofh1; + +close $ofh2; + + + + + + + +=head1 NAME + + + +split-interleaved-fastq.pl - TThis program takes a fastq file containing paired-end reads in interleaved format as input and returns two separate files containing read 1 and read 2 in the correct order. + + + +=head1 SYNOPSIS + + + + perl split-interleaved-fastq.pl --input interleaved_fastq_file.fastq --output output.fastq + + + +=head1 OPTIONS + + + +=over 4 + + + +=item B<--input> + + + +The input file which contains read1 and read2 in a single file in FASTQ format. Mandatory parameter + + + +=item B<--output> + + + +The output file. Mandatory parameter + + + +=item B<--help> + + + +Display help for this script + + + +=back + + + +=head1 Details + + + +=head2 Input + + + +The paired-end reads in interleaved format; input file looks like following: + + + + @fc_HWUSI-EAS613R:1:1:4:682#CATA/1 + + TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG + + +fc_HWUSI-EAS613R:1:1:4:682#CATA/1 + + baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV + + @fc_HWUSI-EAS613R:1:1:4:682#CATA/2 + + TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA + + +fc_HWUSI-EAS613R:1:1:4:682#CATA/2 + + bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + + + +=head2 Output + + + +The output looks like as following for reads 1: + + + + @fc_HWUSI-EAS613R:1:1:4:682#CATA/1 + + TTGTANGATTTCGTCCAGACTTATCTGGAGCATCCGGACGGTCGGGTGAAGCTCAATCCTCAGCTGGTGTTG + + +fc_HWUSI-EAS613R:1:1:4:682#CATA/1 + + baaa\DVbbbbaaaaa`[`abaaaab`b`]aab]_aaa``Z^`a[SN^QR^`]___aXK[a\T\[UTWWMZV + + + +The output looks like as following for reads 2: + + + + @fc_HWUSI-EAS613R:1:1:4:682#CATA/2 + + TCGACAGCTGCTGCTCCGTATTGAGGTACGGATCGTTCACGATCATATACGCCCTCTCTTTCAAAAACCTCA + + +fc_HWUSI-EAS613R:1:1:4:682#CATA/2 + + bbbY`[`a\S_Y][XPaUDZ__LLL]TZPWXBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + + + + + +=head1 AUTHORS + + + +Ram vinay pandey + + + +=cut + + \ No newline at end of file |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/primers/seq_primer_fliC.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/primers/seq_primer_fliC.txt Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,5 @@ +seq_primer_fliC GAAATTCAGGTGCCGATACAAGGG CGCTGCCTTGATTGTGT + + + + |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/primers/seq_primer_fljB.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/primers/seq_primer_fljB.txt Wed Dec 06 15:59:29 2017 -0500 |
| b |
| @@ -0,0 +1,14 @@ +fljB_cornell CCGAATTCATGGCACAAGTAATCAACACTAA CGGGATCCTTAACGTAACACAGACAGCACG + +fljB_CDC1 TGTCGATAACCTGGATGACACAGG GGCATCCAGTGTAGTACCATTATC + +fljB_CDC2 TCGATAACCTGGATGACACAG CATTTACAGCTATACATTCCATAAAGA + +fljB_cornell2 GGCACAAGTAATCAACACTAACA CATTTACAGCCATACATTCCATA + + + + + + + |
| b |
| diff -r 000000000000 -r c577b57b7c74 SeqSero/seqsero.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero/seqsero.xml Wed Dec 06 15:59:29 2017 -0500 |
| [ |
| @@ -0,0 +1,79 @@ +<tool id="seqsero_v1" name="seqsero_v1" version="1.0"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package">biopython</requirement> + <requirement type="package">blast</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">sra-tools</requirement> + <requirement type="package">bwa</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $jobtype.select == "asm" + ln -s $jobtype.draft sample.fasta; + #else if $jobtype.select == "se" + ln -s $jobtype.fastq1 sample_1.fastq; + #else if $jobtype.select == "pe" + ln -s $jobtype.fastq1 sample_1.fastq; + ln -s $jobtype.fastq2 sample_2.fastq; + #end if + + $__tool_directory__/SeqSero.py + #if $jobtype.select == "asm" + -m 4 + -i sample.fasta + #else if $jobtype.select == "se" + -m 3 + -i sample_1.fastq + #else if $jobtype.select == "pe" + -m 2 + -i sample_1.fastq ample_2.fastq + #end if + -b $maptype.select + ; cat SeqSero_result*/Seqsero_result.txt > results.txt; + + ]]></command> + <inputs> + <conditional name="jobtype"> + <param name="select" type="select" label="Assembly or FASTQ Reads?"> + <option value="asm">Genome Assembly</option> + <option value="se">Single-End Reads</option> + <option value="pe">Paired-End Reads</option> + </param> + <when value="asm"> + <param name="draft" type="data" format="fasta" label="FASTA" /> + </when> + <when value="se"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + </when> + <when value="pe"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + <param name="fastq2" type="data" format="fastq" label="FASTQ" /> + </when> + </conditional> + + <conditional name="maptype"> + <param name="select" type="select" label="Algorithms for BWA mapping?"> + <option value="sam">sam</option> + <option value="mem">mem</option> + </param> + </conditional> + + </inputs> + <outputs> + <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/> + </outputs> + <help><![CDATA[ + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015, + title={Salmonella serotype determination utilizing high-throughput genome sequencing data.}, + journal={J Clin Microbiol}, publisher={ASM}, + author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.}, + year={2015}, month={Max}, + url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}}, + }</citation> + </citations> + +</tool> |