NAME

Bio::Tools::Run::PiseApplication::matcher

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::matcher

      Bioperl class for:

	MATCHER	Finds the best local alignments between two sequences (EMBOSS)


      Parameters: 

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


		matcher (String)

		init (String)

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

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

		datafile (Excl)
			Matrix file (-datafile)

		alternatives (Integer)
			Number of alternative matches (-alternatives)

		gappenalty (Integer)
			Gap penalty (-gappenalty)

		gaplength (Integer)
			Gap length penalty (-gaplength)

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

		outfile_aformat (Excl)
			Alignment output format (-aformat)

		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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/matcher.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $matcher = Bio::Tools::Run::PiseApplication::matcher->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::matcher 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 $matcher = $factory->program('matcher');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::matcher.