gdeltaenc

 

Function

Calculate the codon usage bias related to translation optimization (delta ENC)

Description

gdeltaenc calculates the codon usage bias related to translation
optimization (delta ENC) described in Rocha (2004). The basic idea is to
calculate the Effective Number of Codons (ENC) for highly-expressed genes
(ribosomal genes) and weakly-expressed genes (all genes), and taking the
relative difference between them. ENC assigns a gene a number between 20 to
61 where 20 indicates that one codon is used for each aminoacid 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 gdeltaenc

% gdeltaenc refseqn:NC_000913
Calculate the codon usage bias related to translation optimization (delta
ENC)
Program compseq output file [nc_000913.gdeltaenc]: 

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 Program compseq output file Output file <*>.gdeltaenc
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

gdeltaenc reads one or more nucleotide sequences.

Output file format

The output from gdeltaenc is to a plain text file.

File: nc_000913.gdeltaenc

Sequence: NC_000913 DELTA-ENC 0.255663430420712

Data files

None.

Notes

None.

References

   Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy, 
      specialization, and efficient decoding for translation optimization,
      Genome Research, 14(11):2279-2286

   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
gcbi Calculates the codon bias index (CBI)
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.