ggenomemap3

 

Function

Draws the map of the genome (version 3)

Description

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/

Usage

Here is a sample session with ggenomemap3

% ggenomemap3 refseqn:NC_000913
Draws the map of the genome (version 3)
Created ggenomemap3.1.png

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 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

Input file format

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

ggenomemap3 reads one or more nucleotide sequences.

Output file format

The output from ggenomemap3 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
gcircular_map Draws circular map of the genome
gdnawalk Draws DNA Walk map of the genome

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.