gnucleotideperiodicity

 

Function

Checks the periodicity of certain oligonucleotides

Description

gnucleotideperiodicity checks the periodicity of certain nucleotide
(best known with AA dinucleotide). Bacteria and archaebacteria are
known to show periodicity of ApA dinucleotides at about 11bp and 10bp.
Lower eukaryotes also show periodicity but higher eukaryotes do not.

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 gnucleotideperiodicity

% gnucleotideperiodicity refseqn:NC_000913
Checks the periodicity of certain oligonucleotides
Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]: 

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

Example 2
?
% gnucleotideperiodicity refseqn:NC_000913 -plot -graph png
Checks the periodicity of certain oligonucleotides
Created gnucleotideperiodicity.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 <*>.gnucleotideperiodicity
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-format string Output file format. Dependent on 'convert' command Any string png
-window integer Window size to seek periodicity Any integer value 50
-nucleotide string Nucleotide to search Any string aa
-[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

gnucleotideperiodicity reads one or more nucleotide sequences.

Output file format

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

File: nc_000913.gnucleotideperiodicity

Sequence: NC_000913
window,value
0,35134
1,30121
2,25409
3,23508
4,25830
5,25136
6,25658
7,28279

[Part of this file has been deleted for brevity]

40,28042
41,25892
42,25968
43,28240
44,25841
45,25591
46,27788
47,25832
48,25427
49,0

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
gkmertable Create an image showing all k-mer abundance within a sequence
goligomercounter Counts the number of given oligomers in a sequence
goligomersearch Searches oligomers in given sequence
gsignature Calculate oligonucleotide usage (genomic signature)

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.