NAME

Bio::Tools::Run::PiseApplication::wordmatch

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::wordmatch

      Bioperl class for:

	WORDMATCH	Finds all exact matches of a given size between 2 sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/wordmatch.html 
         for available values):


		wordmatch (String)

		init (String)

		asequence (Sequence)
			asequence -- any [single sequence] (-asequence)
			pipe: seqfile

		bsequence (Sequence)
			bsequence [single sequence] (-bsequence)

		wordsize (Integer)
			Word size (-wordsize)

		outfile (OutFile)
			outfile (-outfile)
			pipe: readseq_ok_alig

		outfile_aformat (Excl)
			Alignment output format (-aformat)

		afeatout (OutFile)
			feature file for output aseq (-afeatout)

		afeatout_offormat (Excl)
			Feature output format (-offormat)

		bfeatout (OutFile)
			feature file for output bseq (-bfeatout)

		bfeatout_offormat (Excl)
			Feature output format (-offormat)

		auto (String)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/wordmatch.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $wordmatch = Bio::Tools::Run::PiseApplication::wordmatch->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::wordmatch object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $wordmatch = $factory->program('wordmatch');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::wordmatch.