Bio::Tools::Run::PiseApplication::combat.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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 (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.