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gcbi |
gcbi calculates the codon bias index (CBI) for each gene af the given
genome. CBI is a directional codon bias which measures the usage of
optimal codons in a gene. CBI is similar to Fop, basically taking values
from0 (no bias) and 1 (maximum bias) and can take negative values
depending on the codon usage.
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/
% gcbi refseqn:NC_000913 Calculates the codon bias index (CBI) Codon usage output file [nc_000913.gcbi]: |
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 | <*>.gcbi |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-translate | boolean | Include when translating using standard codon table | Boolean value Yes/No | No |
-delkey | string | Regular expression to delete key | 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
gcbi reads one or more nucleotide sequences.
The output from gcbi is to a plain text file.
File: nc_000913.gcbi
Sequence: NC_000913 cbi,gene 0.8716,thrL 0.3441,thrA 0.3462,thrB 0.4280,thrC 0.3868,yaaX 0.3908,yaaA 0.3521,yaaJ 0.5354,talB [Part of this file has been deleted for brevity] 0.4005,yjjX 0.4388,ytjC 0.3934,rob 0.4645,creA 0.4266,creB 0.3435,creC 0.3796,creD 0.4980,arcA 0.5412,yjjY 0.4018,yjtD |
None.
None.
Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability, J.Mol.Evo,. 37:273-280. 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 |
---|---|
gdeltaenc | Calculate the codon usage bias related to translation optimization (delta ENC) |
gicdi | Calculates the intrinsic codon deviation index (ICDI) |
gsvalue | Calculate the strength of selected codon usage bias (S) |
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