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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
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gbui Function Calculates base usage indices for protein-coding sequences Description gbui calculates base usage indices of protein-coding sequences (excluding start and stop codons) for each gene. Indices calculated are as follows, acgt: Total bumber of bases (A+T+G+C) ryr: Purine/Pyrimidine ratio (A+G)/(T+C) gcc: G+C content (G+C)/(A+T+G+C) Hgc: entropy of G+C content (G+C)/(A+T+G+C) gcs: GC skew (C-G)/(C+G) ats: AT skew (A-T)/(A+T) G-language SOAP service is provided by the Institute for Advanced Biosciences, Keio University. The original web service is located at the following URL: http://www.g-language.org/wiki/soap WSDL(RPC/Encoded) file is located at: http://soap.g-language.org/g-language.wsdl Documentation on G-language Genome Analysis Environment methods are provided at the Document Center http://ws.g-language.org/gdoc/ Usage Here is a sample session with gbui % gbui refseqn:NC_000913 Calculates base usage indices for protein-coding sequences Program compseq output file [nc_000913.gbui]: Go to the input files for this example Go to the output files for this example Command line arguments Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.gbui] Program compseq output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -translate boolean [N] Include when translating using standard codon table -position menu [all] Codon position (Values: all (Assess overall base usage of the gene); 1 (Assess base usage at 1st position of codons); 2 (Assess base usage at 2nd position of codons); 3 (Assess base usage at 3rd position of codons)) -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular expression to delete key (Any string) -[no]accid boolean [Y] Include to use sequence accession ID as query Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format The database definitions for following commands are available at http://soap.g-language.org/kbws/embossrc gbui reads one or more nucleotide sequences. Output file format The output from gbui is to a plain text file. File: nc_000913.gbui Sequence: NC_000913 acgt,ryr,gcc,Hgc,gcs,ats,gene 60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL 2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA 927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB 1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC 291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX 771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA 1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ 948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB [Part of this file has been deleted for brevity] 507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX 642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC 864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob 468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA 684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB 1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC 1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD 711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA 135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY 681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD Data files None. Notes None. References Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. Warnings None. Diagnostic Error Messages None. Exit status It always exits with a status of 0. Known bugs None. See also gdinuc Calculates dinucleotide usage Author(s) Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan History 2012 - Written by Hidetoshi Itaya 2013 - Fixed by Hidetoshi Itaya Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None.