ggcskew

 

Function

Calculates the GC skew of the input sequence

Description

ggcskew calculates and plots the GC skew of the given sequence. The "skew"
of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can
alternatively calculate AT skew, purine skew, and keto skew, as well as
cumulative skew. GC skew is used to observe various biological aspects
such as prediction of replication origin and terminus in bacteria.

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 ggcskew

% ggcskew refseqn:NC_000913
Calculates the GC skew of the input sequence
Program compseq output file (optional) [nc_000913.ggcskew]: 

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

Example 2

% ggcskew refseqn:NC_000913 -plot -graph png
Calculates the GC skew of the input sequence
Created ggcskew.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 <*>.ggcskew
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-window integer Window size to observe Any integer value 10000
-slide integer Window slide size Any integer value 10000
-cumulative boolean Include to calculate cumulative skew Boolean value Yes/No No
-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 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

ggcskew reads one or more nucleotide sequences.

Output file format

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

File: nc_000913.ggcskew

Sequence: NC_000913
location,GC skew
0,-0.035529
10000,-0.039648
20000,-0.049791
30000,0.005072
40000,-0.063483
50000,-0.030256
60000,0.011875
70000,-0.029478

[Part of this file has been deleted for brevity]

4530000,-0.017164
4540000,-0.036140
4550000,-0.028166
4560000,0.012166
4570000,-0.040486
4580000,-0.020692
4590000,-0.043920
4600000,-0.026363
4610000,-0.022778
4620000,-0.049396

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
ggcwin Calculates the GC content along the given genome
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.