gcai

 

Function

Calculate codon adaptation index for each gene

Description

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/

Usage

Here is a sample session with gcai

% gcai refseqn:NC_000913
Calculate codon adaptation index for each gene
Codon usage output file [nc_000913.gcai]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

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

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gcai reads one or more nucleotide sequences.

Output file format

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

Data files

None.

Notes

None.

References

   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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
gp2 Calculate the P2 index of each gene
gphx Identify predicted highly expressed gene

Author(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

History

2012 - Written by Hidetoshi Itaya

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scrips.

Comments

None.