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gscs |
gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS
are calculated using completely synonymous codon usage as the expectation
and then scaled by dividing the value by the number of codons in the gene
excluding Trp and Met.
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/
% gscs refseqn:NC_000913 Calculates the scaled chi-square Codon usage output file [nc_000913.gscs]: |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
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 | <*>.gscs |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-translate | boolean | Include when translates using standard codon table | Boolean value Yes/No | No |
-delkey | string | Regular expression to delete key (i.e. amino acids and nucleotides) | Any string | [^ACDEFGHIKLMNPQRSTVWYacgtU] |
-[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
gscs reads one or more nucleotide sequences.
The output from gscs is to a plain text file.
File: nc_000913.gscs
Sequence: NC_000913 scs,gene 1.4458,thrL 0.3122,thrA 0.2551,thrB 0.4104,thrC 0.3084,yaaX 0.3230,yaaA 0.2957,yaaJ 0.7101,talB [Part of this file has been deleted for brevity] 0.3054,yjjX 0.4076,ytjC 0.4231,rob 0.3903,creA 0.3472,creB 0.2695,creC 0.3500,creD 0.5077,arcA 0.4576,yjjY 0.2926,yjtD |
None.
None.
Comeron JM., Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases, 15(19):8023-40. 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 |
---|---|
genc | Calculate the effective number of codons (Nc) |
gew | Calculate a measure of synonymous codon usage evenness (Ew) |
gfop | Calculate the frequency of optimal codons (Fop) |
gwvalue | Calculate the 'relative adaptiveness of each codon' (W) |
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