gp2

 

Function

Calculate the P2 index of each gene

Description

gp2 calculates the P2 index for each gene. This index describes
the proportion of codons conforming to the intermediate strength of
codon-anticodon interaction energy rule of Grosjean and Fiers:
P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.
It indicates the efficiency of the codon-anticodon interaction, and has
been used as an indicator of the presence of translational selection.

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 gp2

% gp2 refseqn:NC_000913
Calculate the P2 index of each gene
Codon usage output file [nc_000913.gp2]: 

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 <*>.gp2
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-[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

gp2 reads one or more nucleotide sequences.

Output file format

The output from gp2 is to a plain text file.

File: nc_000913.gp2

Sequence: NC_000913
P2,gene
0.4444,thrL
0.4234,thrA
0.4565,thrB
0.5156,thrC
0.4074,yaaX
0.4494,yaaA
0.3621,yaaJ
0.6832,talB

[Part of this file has been deleted for brevity]

0.3692,yjjX
0.4912,ytjC
0.4271,rob
0.4318,creA
0.3065,creB
0.3851,creC
0.4320,creD
0.6395,arcA
0.7857,yjjY
0.3333,yjtD

Data files

None.

Notes

None.

References

   Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
      expressivity, Nucleic Acids Res, 10(22):7055-74.

   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
gcai Calculate codon adaptation index for 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.