gcircularmap

 

Function

Draws circular map of the genome

Description

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/

Usage

Here is a sample session with gcircularmap

% gcircularmap refseqn:NC_000913
Draws circular map of the genome
Created gcircularmap.1.svg

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 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

Input file format

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

gcircularmap reads one or more nucleotide sequences.

Output file format

The output from gcircularmap 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
gdnawalk Draws DNA Walk map of the genome
ggenomemap3 Draws the map of the genome (version 3)

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.