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gcircularmap |
gdnawalk creates a circular map of the genome using SVG, suitable for
plasmids and circular bacterial chromosomes.
From the outer ring inwards, genes on direct strand (pink),
genes on complementary strand (yellow), tRNAs (green arrows),
rRNAs (pink or orange stripes depending on the strand),
GC content (brown lines), GC skew (yellow lines). Replication
origin and terminus predicted from the GC skew shift points
are also labeled.
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/
% gcircularmap refseqn:NC_000913 Draws circular map of the genome Created gcircularmap.1.svg |
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 | svg |
-[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 | gcircularmap |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gcircularmap reads one or more nucleotide sequences.
The output from gcircularmap 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 |
---|---|
gdnawalk | Draws DNA Walk map of the genome |
ggenomemap3 | Draws the map of the genome (version 3) |
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