NAME

Bio::Tools::Run::PiseApplication::combat

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::combat

      Bioperl class for:

        COMBAT  Comparison of coding DNA (Pedersen, Lyngso,Hein)

        References:

                Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998.



      Parameters: 

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


                combat (String)

                sequence1 (Sequence)
                        First Sequence

                sequence2 (Sequence)
                        Second Sequence

                output_aln (OutFile)

                alignment_file (OutFile)
                        pipe: readseq_ok_alig

                protein_distance_matrix (Excl)
                        Amino-acid distance matrix

                nucleotide_distance_matrix (Excl)
                        Nucleotid distance matrix

                protein_gap_open (Integer)
                        Gap open cost for protein

                protein_gap_ext (Integer)
                        Gap extension cost for protein

                dna_gap_open (Integer)
                        Gap open cost for dna

                dna_gap_ext (Integer)
                        Gap extension cost for dna

                gnuplot_call (String)

                gnuplot_commands (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/combat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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