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gfop |
gfop calculates the frequency of optimal codons (Fop).Fop is an index to
show the optimization level of synonymous codon usage choice. It is
basically a ratio of optimal codons against all codons used. The value
of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
codons are used).
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/
% gfop refseqn:NC_000913 Calculate the frequency of optimal codons (Fop) Codon usage output file [nc_000913.gfop]: |
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 | <*>.gfop |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-translate | boolean | Include when translates using standard codon table | Boolean value Yes/No | No |
-[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
gfop reads one or more nucleotide sequences.
The output from gfop is to a plain text file.
File: nc_000913.gfop
Sequence: NC_000913 Laa,Lc,fop,gene 20,5,0.4000,thrL 819,133,0.4361,thrA 309,46,0.4783,thrB 427,69,0.5217,thrC 97,7,0.2857,yaaX 257,56,0.4643,yaaA 475,96,0.3958,yaaJ 316,56,0.6964,talB [Part of this file has been deleted for brevity] 169,27,0.2593,yjjX 214,23,0.5652,ytjC 288,49,0.4082,rob 156,23,0.3478,creA 228,26,0.3462,creB 473,69,0.3478,creC 449,70,0.3286,creD 237,46,0.6957,arcA 45,10,0.7000,yjjY 227,24,0.2500,yjtD |
None.
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Ikemura, T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J.Mol.Biol, 151:389-409. Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular organisms, Mol.Biol.Evol, 2(1):13-34. 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) |
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