![]() |
gwvalue |
gwvalue calculates the 'relative adaptiveness of each codon' (W value)
which is essential in CAI analysis. W value is calculated by setting the
best codon to 1 and calculating the proportion of the other codons.
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/
% gwvalue refseqn:NC_000913 Calculate the 'relative adaptiveness of each codon' (W) Codon usage output file [nc_000913.gwvalue]: |
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 | <*>.gwvalue |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-include | string | Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al. | Any string | ribosomal.*protein |
-exclude | string | Regular expression to exclude genes from a reference set | Any string | [Mm]itochondrial |
-[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
gwvalue reads one or more nucleotide sequences.
The output from gwvalue is to a plain text file.
File: nc_000913.gwvalue
Sequence: NC_000913 Reference set of highly expressed genes product 30S ribosomal subunit protein S20 30S ribosomal subunit protein S2 ribosomal protein S12 methylthiotransferase; radical SAM superfamily ribosomal protein S6 modification protein 30S ribosomal subunit protein S1 ribosomal-protein-S5-alanine N-acetyltransferase 50S ribosomal subunit protein L32 [Part of this file has been deleted for brevity] T,acc,1.0000 T,acg,0.2234 T,act,0.9734 V,gta,0.4960 V,gtc,0.2281 V,gtg,0.3422 V,gtt,1.0000 W,tgg,1.0000 Y,tac,1.0000 Y,tat,0.5310 |
None.
None.
Sharp PM et al. (2005) Variation in the strength of selected codon usage bias among bacteria, Nucleic Acids Res. 33(4):1141-1153 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170. Nakamura and Tabata (1997) Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes, Microb.Comp.Genomics 2:299-312. Sharp and Li (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res. 15:1281-1295. 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) |
gscs | Calculates the scaled chi-square |
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