ggenomicskew

 

Function

Calculates the GC skew in different regions of the given genome

Description

ggenomicskew calculates and plots the GC skew for the whole genome, coding
regions, intergenic regions, and the third codon. This program is useful in
visualizing various base composition bias within the genome. AT skew can be
calculated instead of GC skew by toggling the -at qualifier.

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 ggenomicskew

% ggenomicskew refseqn:NC_000913
Calculates the GC skew in different regions of the given genome
Program compseq output file (optional) [nc_000913.ggenomicskew]: 

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

Example 2

% ggenomicskew refseqn:NC_000913 -plot -graph png
Calculates the GC skew in different regions of the given genome
Created ggenomicskew.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 <*>.ggenomicskew
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-divide integer Window to divide into Any integer value 250
-at boolean Input 1 when observing AT skew instead of GC skew Boolean value Yes/No No
-[no]accid boolean Include to use sequence accession ID as query Boolean value Yes/No Yes
-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

ggenomicskew reads one or more nucleotide sequences.

Output file format

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

File: nc_000913.ggenomicskew

Sequence: NC_000913
location,GC skew,coding,intergenic,third codon
0,-0.036259,-0.040085,-0.034707,-0.141888,
1,-0.031167,-0.035657,0.047953,-0.175758,
2,-0.028670,-0.031139,-0.049143,-0.018466,
3,-0.016647,-0.004656,-0.102616,0.086181,
4,-0.041985,-0.029846,-0.088670,0.015291,
5,-0.097093,-0.103813,-0.067275,-0.247401,
6,-0.028028,-0.016363,-0.048806,-0.047332,
7,-0.055805,-0.059329,-0.020071,-0.123271,

[Part of this file has been deleted for brevity]

241,0.000772,-0.012151,-0.063786,0.069585,
242,-0.025787,-0.000384,-0.049143,0.029431,
243,0.010516,0.008217,-0.030600,0.128657,
244,-0.037115,-0.015134,0.017500,0.035398,
245,-0.000317,0.006021,-0.047170,0.091549,
246,-0.025417,-0.015190,-0.116608,0.044619,
247,-0.038404,-0.035676,-0.135714,0.015375,
248,-0.026246,-0.024240,-0.037190,-0.130118,
249,-0.053371,-0.057225,-0.022472,-0.082167,
250,-0.026316,0.166667,-0.151515,0.000000,

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
ggcwin Calculates the GC content along the given genome
ggeneskew Calculate the gene strand bias 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.