gcbi

 

Function

Calculates the codon bias index (CBI)

Description

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/

Usage

Here is a sample session with gcbi

% gcbi refseqn:NC_000913
Calculates the codon bias index (CBI)
Codon usage output file [nc_000913.gcbi]: 

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 <*>.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

Input file format

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

gcbi reads one or more nucleotide sequences.

Output file format

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

Data files

None.

Notes

None.

References

   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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

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)

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.