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ggenomemap3 |
ggenomemap3 creates a map of the genome, showing the local nucleotide
contents and positions of genes. A is shown in red, T is shown in green,
G is shown in yellow, and C is shown in blue.
Created image has a resolution of 8192x8192 and is suited for conversion
to SVG, which can be performed by specifying the -format option. The formats
available are dependent to the "convert" command from ImageMagick.
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/
% ggenomemap3 refseqn:NC_000913 Draws the map of the genome (version 3) Created ggenomemap3.1.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 | Image width | Any integer value | 8192 |
-height | integer | Image height | Any integer value | 8192 |
-[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes |
-goutfile | string | Output file for non interactive displays | Any string | ggenomemap3 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
ggenomemap3 reads one or more nucleotide sequences.
The output from ggenomemap3 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 |
---|---|
gcircular_map | Draws circular map of the genome |
gdnawalk | Draws DNA Walk map of the genome |
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