genc

 

Function

Calculate the effective number of codons (Nc)

Description

genc calculates the effective number of codons (ENC|Nc). ENC is a measure
for species-independent codon usage bias. Some measures including CAI are
species-dependent as optimal codons differ. ENC assigns a gene a number
between 20 to 61 where 20 indicates that one codon is used for each amino
acid and 61 indicates that each codon is used equally throughout the
protein sequence.

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 genc

% genc refseqn:NC_000913
Calculate the effective number of codons (Nc)
Codon usage output file [nc_000913.genc]: 

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 <*>.genc
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

genc reads one or more nucleotide sequences.

Output file format

The output from genc is to a plain text file.

File: nc_000913.genc

Sequence: NC_000913
enc,gene
,thrL
48.41,thrA
54.13,thrB
46.18,thrC
51.65,yaaX
45.71,yaaA
48.54,yaaJ
36.83,talB

[Part of this file has been deleted for brevity]

51.43,yjjX
46.61,ytjC
49.83,rob
47.74,creA
50.63,creB
51.39,creC
48.42,creD
41.53,arcA
61,yjjY
53.63,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.

   Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
      87:23-29.

   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
gew Calculate a measure of synonymous codon usage evenness (Ew)
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.