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gcai |
gcai calculates codon adaptation index (CAI) for each gene. CAI is measure
a of the relative adaptiveness of the codon usage of a gene towards the
codon usage of highly expressed genes, ranging from 0 (no bias) to 1
(maximum bias). CAI can be used as a 'universal' measure of codon usage
bias as it is correlated with various gene features such as gene expression
level, GC content, and GC skew.
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/
% gcai refseqn:NC_000913 Calculate codon adaptation index for each gene Codon usage output file [nc_000913.gcai]: |
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 | <*>.gcai |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-translate | boolean | Include when translating using standard codon table | Boolean value Yes/No | No |
-wabsent | string | W value of codons absent from a reference set to negative when excludes such codons from the calculation | Any string | -1 |
-[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
gcai reads one or more nucleotide sequences.
The output from gcai is to a plain text file.
File: nc_000913.gcai
Sequence: NC_000913 cai,gene 0.7256,thrL 0.4831,thrA 0.4719,thrB 0.5178,thrC 0.4989,yaaX 0.4933,yaaA 0.4533,yaaJ 0.7074,talB [Part of this file has been deleted for brevity] 0.4681,yjjX 0.4797,ytjC 0.5350,rob 0.4932,creA 0.3918,creB 0.4170,creC 0.4167,creD 0.6466,arcA 0.4236,yjjY 0.3913,yjtD |
None.
None.
Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15(3):1281-95. 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 |
---|---|
gp2 | Calculate the P2 index of 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