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gcgr |
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/
% gcgr refseqn:NC_000913 Create a Chaos Game Representation of a given sequence Created gcgr.1.png |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gcgr reads one or more nucleotide sequences.
The output from gcgr is to an image file.
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
gseq2png | Converts a sequence to PNG image |
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