NAME

Bio::Tools::Run::PiseApplication::supermatcher

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::supermatcher

      Bioperl class for:

	SUPERMATCHER	Finds a match of a large sequence against one or more sequences (EMBOSS)


      Parameters: 

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


		supermatcher (String)

		init (String)

		seqa (Sequence)
			seqa -- any [sequences] (-seqa)
			pipe: seqsfile

		seqb (Sequence)
			seqb [set of sequences] (-seqb)

		gapopen (Float)
			Gap opening penalty (-gapopen)

		gapextend (Float)
			Gap extension penalty (-gapextend)

		datafile (Excl)
			Matrix file (-datafile)

		width (Integer)
			Alignment width (-width)

		wordlen (Integer)
			word length for initial matching (-wordlen)

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

		outfile_aformat (Excl)
			Alignment output format (-aformat)

		errorfile (OutFile)
			Error file to be written to (-errorfile)

		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/supermatcher.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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