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gp2 |
gp2 calculates the P2 index for each gene. This index describes
the proportion of codons conforming to the intermediate strength of
codon-anticodon interaction energy rule of Grosjean and Fiers:
P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.
It indicates the efficiency of the codon-anticodon interaction, and has
been used as an indicator of the presence of translational selection.
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/
% gp2 refseqn:NC_000913 Calculate the P2 index of each gene Codon usage output file [nc_000913.gp2]: |
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 | <*>.gp2 |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-[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
gp2 reads one or more nucleotide sequences.
The output from gp2 is to a plain text file.
File: nc_000913.gp2
Sequence: NC_000913 P2,gene 0.4444,thrL 0.4234,thrA 0.4565,thrB 0.5156,thrC 0.4074,yaaX 0.4494,yaaA 0.3621,yaaJ 0.6832,talB [Part of this file has been deleted for brevity] 0.3692,yjjX 0.4912,ytjC 0.4271,rob 0.4318,creA 0.3065,creB 0.3851,creC 0.4320,creD 0.6395,arcA 0.7857,yjjY 0.3333,yjtD |
None.
None.
Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Res, 10(22):7055-74. 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 |
---|---|
gcai | Calculate codon adaptation index for each gene |
gphx | Identify predicted highly expressed gene |
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