gcgr

 

Function

Create a Chaos Game Representation of a given sequence

Description

gcgr creates a Chaos Game Representation (CGR) image of a given sequence. CGR is generated by the following procedure:

1. Start from position (0,0) or the origin of two dimensional coordinate.
Four nucleotides are located at the four corners:
A: (-1, 1) upper left
T: (1, -1) lower right
G: (1, 1) upper right
C: (-1, -1) lower left
2. For each nucleotide, move and mark the new location which is halfway
between the current location and the nucleotide.
For example, if the first letter is A, position is moved from (0,0) to
midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).

3. Repeat this procedure for all nucleotides.
CGR is a generalized scale-independent Markov probability table for the
sequence, and oligomer tables can be deduced from CGR image.

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 gcgr

% gcgr refseqn:NC_000913
Create a Chaos Game Representation of a given sequence
Created gcgr.1.png

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
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-format string Output file format. Dependent on 'convert' command Any string png
-width integer Width of image Any integer value 1024
-goutfile string Output file for non interactive displays Any string gcgr

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gcgr reads one or more nucleotide sequences.

Output file format

The output from gcgr is to an image file.

Data files

None.

Notes

None.

References

   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
gseq2png Converts a sequence to PNG image

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.