gwvalue

 

Function

Calculate the 'relative adaptiveness of each codon' (W)

Description

gwvalue calculates the 'relative adaptiveness of each codon' (W value)
which is essential in CAI analysis. W value is calculated by setting the
best codon to 1 and calculating the proportion of the other codons.

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 gwvalue

% gwvalue refseqn:NC_000913
Calculate the 'relative adaptiveness of each codon' (W)
Codon usage output file [nc_000913.gwvalue]: 

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 <*>.gwvalue
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-include string Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al. Any string ribosomal.*protein
-exclude string Regular expression to exclude genes from a reference set Any string [Mm]itochondrial
-[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

gwvalue reads one or more nucleotide sequences.

Output file format

The output from gwvalue is to a plain text file.

File: nc_000913.gwvalue

Sequence: NC_000913
Reference set of highly expressed genes
product
30S ribosomal subunit protein S20
30S ribosomal subunit protein S2
ribosomal protein S12 methylthiotransferase; radical SAM superfamily
ribosomal protein S6 modification protein
30S ribosomal subunit protein S1
ribosomal-protein-S5-alanine N-acetyltransferase
50S ribosomal subunit protein L32

[Part of this file has been deleted for brevity]

T,acc,1.0000
T,acg,0.2234
T,act,0.9734
V,gta,0.4960
V,gtc,0.2281
V,gtg,0.3422
V,gtt,1.0000
W,tgg,1.0000
Y,tac,1.0000
Y,tat,0.5310

Data files

None.

Notes

None.

References

   Sharp PM et al. (2005) Variation in the strength of selected codon usage
      bias among bacteria, Nucleic Acids Res. 33(4):1141-1153

   Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
      conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.

   Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
      codon usage trends in seven microbial genomes, Microb.Comp.Genomics
      2:299-312.

   Sharp and Li (1987) The codon Adaptation Index--a measure of directional
      synonymous codon usage bias, and its potential applications, Nucleic
      Acids Res. 15:1281-1295.

   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)
gew Calculate a measure of synonymous codon usage evenness (Ew)
gfop Calculate the frequency of optimal codons (Fop)
gscs Calculates the scaled chi-square

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.