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gew |
gew calculates the 'weighted sum of relative entropy' (Ew) as a measure
of synonymous codon usage evenness for each gene. This index takes all
three aspects of amino acid usage (number of distinct amino acids,
relatieve frequencies, and degree of codon degeneracy) into account.
The values range from 0 (no bias) to 1 (maximum bias).
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/
% gew refseqn:NC_000913 Calculate a measure of synonymous codon usage evenness (Ew) Codon usage output file [nc_000913.gew]: |
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 | <*>.gew |
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
gew reads one or more nucleotide sequences.
The output from gew is to a plain text file.
File: nc_000913.gew
Sequence: NC_000913 Ew,gene 0.2800,thrL 0.8458,thrA 0.8292,thrB 0.7937,thrC 0.7032,yaaX 0.7922,yaaA 0.8100,yaaJ 0.6685,talB [Part of this file has been deleted for brevity] 0.7943,yjjX 0.7265,ytjC 0.7932,rob 0.7498,creA 0.7967,creB 0.8490,creC 0.7979,creD 0.6826,arcA 0.6475,yjjY 0.7729,yjtD |
None.
None.
Suzuki H. et al. (2004) The 'weighted sum of relative entropy': a new index for synonymous codon usage bias, Gene, 23;335:19-23. Suzuki H. et al. (2007) Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria, EURASIP J Bioinform Syst Biol, 2007:61374. 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) |
gfop | Calculate the frequency of optimal codons (Fop) |
gscs | Calculates the scaled chi-square |
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