ggcwin

 

Function

Calculates the GC content along the given genome

Description

ggcwin calculates and plots the GC content of the given sequence.

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 ggcwin

% ggcwin refseqn:NC_000913
Calculates the GC content along the given genome
Program compseq output file (optional) [nc_000913.ggcwin]: 

Go to the input files for this example
Go to the output files for this example

Example 2
% ggcwin refseqn:NC_000913 -plot -graph png Calculates the GC content along the given genome Created ggcwin.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
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg EMBOSS_GRAPHICS value, or x11
-outfile outfile Program compseq output file (optional) Output file <*>.ggcwin
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-window integer Window size to observe Any integer value 10000
-at boolean Include for observing AT skew instead of GC skew Boolean value Yes/No No
-purine boolean Include for observing purine (AG/TC) skew Boolean value Yes/No No
-keto boolean Include for observing keto (TG/AC) skew default: "0 Boolean value Yes/No No
-plot toggle Include to plot result Toggle value Yes/No No

Input file format

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

ggcwin reads one or more nucleotide sequences.

Output file format

The output from ggcwin is to a plain text file or the EMBOSS graphics device.

File: nc_000913.ggcwin

Sequence: NC_000913
location,GC content
0,0.520700
10000,0.499400
20000,0.526200
30000,0.532300
40000,0.527700
50000,0.515600
60000,0.555800
70000,0.536000

[Part of this file has been deleted for brevity]

4530000,0.442800
4540000,0.487000
4550000,0.507700
4560000,0.509600
4570000,0.444600
4580000,0.531600
4590000,0.512300
4600000,0.504500
4610000,0.535600
4620000,0.546600

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
ggcskew Calculates the GC skew of the input sequence
ggeneskew Calculate the gene strand bias of the given genome
ggenomicskew Calculates the GC skew in different regions of the given 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.