NAME

Bio::Tools::Run::PiseApplication::map

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::map

      Bioperl class for:

	MAP	Multiple Alignment Program


      Parameters: 

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


		map (String)

		seq (Sequence)
			Sequences File

		gap_size (Integer)
			gap size: minimum length of any gap in a short sequence charged with a constant gap penalty (gs)

		mismatch (Integer)
			score of a mismatch (<0)

		gapopen (Integer)
			gap open penalty (>=0)

		gapext (Integer)
			gap extension penalty (>=0)

		matrix (InFile)
			Matrix (Name of a file containing an alternate or user-defined scoring matrix)

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/map.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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