goligomercounter

 

Function

Counts the number of given oligomers in a sequence

Description

goligomercounter counts the number of oligomers in a sequence (by windows
optionally). Oligomer can be specified using degenerate nucleotide alphabet,
or by regular expressions. k-mers can be counted by specifying the "-length"
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 goligomercounter

% goligomercounter refseqn:NC_000913 atgcatgc
Counts the number of given oligomers in a sequence
Program compseq output file [nc_000913.goligomercounter]: 

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
[-oligomer]
(Parameter 2)
string Oligomer to count Any string  
[-outfile]
(Parameter 3)
outfile Program compseq output file Output file <*>.goligomercounter
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-window integer Int window size Any integer value 0
-[no]accid boolean Include to use sequence accession ID as query Boolean value Yes/No Yes

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

goligomercounter reads one or more nucleotide sequences.

Output file format

The output from goligomercounter is to a plain text file.

File: nc_000913.goligomercounter

Sequence: NC_000913 Oligomer: atgcatgc Number: 27

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
gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
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.