ggeneskew

 

Function

Calculate the gene strand bias of the given genome

Description

ggeneskew calculates and plots the strand bias of genes (or the GC skew
within them). By default, this program visualizes the gene strand preference
(1 for direct, -1 for complement strand), but by specifying -base option
option, GC/AT/Purine/Keto skews of the coding regions or more specifically
in the GC3 (third codon position) with -gctri option can be calculated.

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 ggeneskew

% ggeneskew refseqn:NC_000913
Calculate the gene strand bias of the given genome
Program compseq output file (optional) [nc_000913.ggeneskew]: 

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

Example 2

% ggeneskew refseqn:NC_000913 -plot -graph png
Calculate the gene strand bias of the given genome
Created ggeneskew.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 <*>.ggeneskew
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 Input 1 to calculate cumulative skew Boolean value Yes/No No
-base selection Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews Choose from selection list of values none
-gctri boolean Include to use only the third codon positions 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

ggeneskew reads one or more nucleotide sequences.

Output file format

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

File: nc_000913.ggeneskew

Sequence: NC_000913
location,gene None skew
190,0.294118
337,-0.058914
2801,-0.120000
3734,-0.070588
5234,0.037500
5683,0.020725
6529,0.032765
8238,-0.028226

[Part of this file has been deleted for brevity]

4631820,-0.093407
4632464,-0.006479
4633544,-0.120690
4634030,-0.060367
4634719,-0.104167
4636201,-0.144560
4637613,0.010929
4638425,0.200000
4638965,-0.081871
,

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
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.