gviewcds

 

Function

Displays a graph of nucleotide contents around start and stop codons

Description

gviewcds creates a graph showing the average A,T,G,C contents
around start/stop codons. This is useful to view consensus around
start/stop codons and to find characteristic pattern in CDS.

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 gviewcds

% gviewcds refseqn:NC_000913
Displays a graph of nucleotide contents around start and stop codons
Program compseq output file (optional) [nc_000913.gviewcds]: 

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

Example 2
% gviewcds refseqn:NC_000913 -plot -graph png Displays a graph of nucleotide contents around start and stop codons Created gviewcds.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 <*>.gviewcds
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-length integer Length in bases to show around start/stop codons Any integer value 100
-gap integer Gap shown in graph in between start/stop codon neighbors Any integer value 3
-[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

gviewcds reads one or more nucleotide sequences.

Output file format

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

File: nc_000913.gviewcds

Sequence: NC_000913
position,A,T,G,C
1,28.20,27.60,22.18,22.02
2,26.05,26.81,23.06,24.08
3,27.34,27.37,23.94,21.35
4,26.28,28.83,23.01,21.88
5,26.72,28.22,22.18,22.88
6,26.42,26.72,24.96,21.90
7,27.21,28.66,21.95,22.18
8,25.47,28.39,23.06,23.08

[Part of this file has been deleted for brevity]

400,26.60,27.44,22.67,23.27
401,24.38,26.63,25.05,23.92
402,25.03,26.37,23.71,24.87
403,25.96,27.53,22.53,23.96
404,26.63,25.52,24.17,23.66
405,25.68,26.26,23.50,24.54
406,24.94,26.86,23.92,24.26
407,25.54,26.28,23.73,24.43
408,25.28,26.93,24.38,23.39
409,26.63,26.46,22.32,24.57

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
gbasecounter Creates a position weight matrix of oligomers around start codon
gbasezvalue Extracts conserved oligomers per position using Z-score

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.