gicdi

 

Function

Calculates the intrinsic codon deviation index (ICDI)

Description

gphx calculates codon usage differences between gene classes for identifying
Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is
identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's
nature. PHX genes are known to generally have favorable codon usage, strong
SD sequences, and probably stronger conservation of promoter sequences.
A gene is idenfitied as PA if BgC and BgH is greater than the median of
BgC for every gene with a length close to the gene.

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 gicdi

% gicdi refseqn:NC_000913
Calculates the intrinsic codon deviation index (ICDI)
Codon usage output file [nc_000913.gicdi]: 

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 <*>.gicdi
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-translate boolean Include when translating using standard codon table Boolean value Yes/No No
-delkey string Regular expression to delete key 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

gicdi reads one or more nucleotide sequences.

Output file format

The output from gicdi is to a plain text file.

File: nc_000913.gicdi

Sequence: NC_000913
icdi,gene
0.8192,thrL
0.1258,thrA
0.1127,thrB
0.1689,thrC
0.3099,yaaX
0.2030,yaaA
0.1600,yaaJ
0.3533,talB

[Part of this file has been deleted for brevity]

0.2203,yjjX
0.2719,ytjC
0.1377,rob
0.2647,creA
0.1944,creB
0.1733,creC
0.1926,creD
0.2728,arcA
0.5171,yjjY
0.2434,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.

   Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
      yeast cytochrome c-encoding genes, Gene, 139:43-49.

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