gew

 

Function

Calculate a measure of synonymous codon usage evenness (Ew)

Description

gew calculates the 'weighted sum of relative entropy' (Ew) as a measure
of synonymous codon usage evenness for each gene. This index takes all
three aspects of amino acid usage (number of distinct amino acids,
relatieve frequencies, and degree of codon degeneracy) into account.
The values range from 0 (no bias) to 1 (maximum bias).

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 gew

% gew refseqn:NC_000913
Calculate a measure of synonymous codon usage evenness (Ew)
Codon usage output file [nc_000913.gew]: 

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 <*>.gew
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-translate boolean Include when translates using standard codon table Boolean value Yes/No No
-delkey string Regular expression to delete key (i.e. amino acids and nucleotides) 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

gew reads one or more nucleotide sequences.

Output file format

The output from gew is to a plain text file.

File: nc_000913.gew

Sequence: NC_000913
Ew,gene
0.2800,thrL
0.8458,thrA
0.8292,thrB
0.7937,thrC
0.7032,yaaX
0.7922,yaaA
0.8100,yaaJ
0.6685,talB

[Part of this file has been deleted for brevity]

0.7943,yjjX
0.7265,ytjC
0.7932,rob
0.7498,creA
0.7967,creB
0.8490,creC
0.7979,creD
0.6826,arcA
0.6475,yjjY
0.7729,yjtD

Data files

None.

Notes

None.

References

   Suzuki H. et al. (2004) The 'weighted sum of relative entropy': a new
      index for synonymous codon usage bias, Gene, 23;335:19-23.

   Suzuki H. et al. (2007) Variation in the correlation of G + C composition
      with synonymous codon usage bias among bacteria, EURASIP J Bioinform
      Syst Biol, 2007:61374.

   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
genc Calculate the effective number of codons (Nc)
gfop Calculate the frequency of optimal codons (Fop)
gscs Calculates the scaled chi-square
gwvalue Calculate the 'relative adaptiveness of each codon' (W)

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.