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gcodoncompiler |
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/
% gcodoncompiler refseqn:NC_000913 Calculate various kinds of amino acid and codon usage data Codon usage output file [nc_000913.gcodoncompiler]: |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||
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Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||
[-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | ||||||||||||||||||||||||||||
[-outfile] (Parameter 2) |
outfile | Codon usage output file | Output file | <*>.gcodoncompiler | ||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||
-translate | boolean | Include to translate using standard codon table | Boolean value Yes/No | No | ||||||||||||||||||||||||||||
-startcodon | boolean | Include to include start codon | Boolean value Yes/No | No | ||||||||||||||||||||||||||||
-stopcodon | boolean | Include to include stop codon | Boolean value Yes/No | No | ||||||||||||||||||||||||||||
-delkey | string | Regular expression to delete key (i.e. amino acids and nucleotides) | Any string | [^ACDEFGHIKLMNPQRSTVWYacgtU] | ||||||||||||||||||||||||||||
-data | list | Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene |
|
R0 | ||||||||||||||||||||||||||||
-[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gcodoncompiler reads one or more nucleotide sequences.
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, |
None.
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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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
gaminoinfo | Prints out basic amino acid sequence statistics |
gaaui | Calculates various indece of amino acid usage |
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