gpalindrome

 

Function

Searches palindrome sequences

Description

gpalindrome searches for palindrome sequences in the genome.
Search parameters can be changed for more efficient searches, and g-t
matching can be specified by passing the "-gtmatch" 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 gpalindrome

% gpalindrome refseqn:NC_000913
Searches palindrome sequences
Program compseq output file [nc_000913.gpalindrome]: 

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
[-outfile]
(Parameter 2)
outfile Program compseq output file Output file <*>.gpalindrome
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-shortest integer Shortest palindrome to search Any integer value 4
-loop integer Longest stem loop to allow Any integer value 0
-gtmatch boolean If 1, allows g-t match Boolean value Yes/No No
-[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

gpalindrome reads one or more nucleotide sequences.

Output file format

The output from gpalindrome is to a plain text file.

File: nc_000913.gpalindrome

Sequence: NC_000913
Length, start, end, sequence
4,16,18,tg ca
4,27,29,at at
4,44,46,tt aa
4,67,69,ag ct
4,97,99,aa tt
4,99,101,tt aa
10,100,108,taaaa tttta
4,132,134,tt aa

[Part of this file has been deleted for brevity]

4,4639484,4639486,tg ca
6,4639487,4639491,aag ctt
4,4639495,4639497,cg cg
4,4639506,4639508,ca tg
6,4639552,4639556,gtc gac
4,4639607,4639609,tg ca
4,4639619,4639621,tg ca
4,4639621,4639623,ca tg
4,4639625,4639627,at at
4,4639637,4639639,at at

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
gconsensusz Calculate consensus in given array of sequences
gdistincc Calculates the distance between two loci in circular chromosomes
gseqinfo Prints out basic nucleotide sequence statistics

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.