gdnawalk

 

Function

Draws DNA Walk map of the genome

Description

gdnawalk draws the DNA Walk map of the given genome. DNA Walk is drawn by
moving a single pixel per nucleotide, in the direction specified for each
base. Here A is moved upward, T downward, G to the right, and C to the
left. Position zero (first letter of the genome) is indicated by the
crossing of thin axes.

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 gdnawalk

% gdnawalk refseqn:NC_000913
Draws DNA Walk map of the genome
Created gdnawalk.1.png

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 png
-goutfile string Output file for non interactive displays Any string gdnawalk

Input file format

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

gdnawalk reads one or more nucleotide sequences.

Output file format

The output from gdnawalk 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
gcircularmap Draws circular 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.