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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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gcodoncompiler Function Calculate various kinds of amino acid and codon usage data Description gcodoncompiler calculates various kinds of amino acid and codon usage data. The following values are calculable: A0: Absolute amino acid frequency A1: Relative amino acid frequency C0: Absolute codon frequency C1: Relative codon frequency in a complete sequence C2: Relative codon frequency in each amino acid C3: Relative synonymous codon usage C4: Relative adaptiveness C5: Maximum or minor codon For amino acids unpresent in a gene, C2-C3 does not calculate the values. By using R* in place, such values are hypothesized that alternative synonymous codons are used with equal frequency. 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 gcodoncompiler % gcodoncompiler refseqn:NC_000913 Calculate various kinds of amino acid and codon usage data Codon usage output file [nc_000913.gcodoncompiler]: 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 [*.gcodoncompiler] Codon usage output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -translate boolean [N] Include to translate using standard codon table -startcodon boolean [N] Include to include start codon -stopcodon boolean [N] Include to include stop codon -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular expression to delete key (i.e. amino acids and nucleotides) (Any string) -data menu [R0] Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene (Values: A0 (Absolute amino acid frequency ('AA')); A1 (Relative amino acid frequency ('RAAU')); C0 (Absolute codon frequency ('AF')); C1 (Relative codon frequency in a complete sequence); C2 (Relative codon frequency in each amino acid ('RF')); C3 (Relative synonymous codon usage ('RSCU')); C4 (Relative adaptiveness); i.e., ratio to maximum of minor codon ('W') C5 (Maximum (1) or minor (0) codon); R0 (Absolute codon frequency ('AF')); R1 (Relative codon frequency in a complete sequence); R2 (Relative codon frequency in each amino acid ('RF')); R3 (Relative synonymous codon usage ('RSCU')); R4 (Relative adaptiveness); i.e., ratio to maximum of minor codon ('W') R5 (Maximum (1) or minor (0) codon)) -[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 gcodoncompiler reads one or more nucleotide sequences. Output file format The output from gcodoncompiler is to a plain text file. File: nc_000913.gcodoncompiler Sequence: NC_000913 Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag 26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069, 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 gaminoinfo Prints out basic amino acid sequence statistics gaaui Calculates various indece of amino acid 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.