NAME

Bio::Tools::Run::PiseApplication::patser

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::patser

      Bioperl class for:

        PATSER  score the words of a sequence against an alignment matrix (Hertz, Storm)


      Parameters: 

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


                patser (String)

                matrix (InFile)
                        Matrix file (-m)
                        pipe: consensus_matrix

                sequence (Sequence)
                        Sequences file

                weight (Switch)
                        Matrix is a weight matrix (-w)

                vertical (Switch)
                        Matrix is a vertical matrix (-v)

                correction (Integer)
                        Correction added to the elements of the alignment matrix (-b)

                print_matrix (Switch)
                        Print the weight matrix derived from the alignment matrix (-p)

                dna (Switch)
                        Alphabet and normalization information for DNA

                protein (Switch)
                        Alphabet and normalization information for protein

                ascii_alphabet (InFile)
                        Alphabet and normalization information (-a)

                score (Excl)
                        Score options (-d)

                range (Integer)
                        Range for approximating a weight matrix with integers (-R)

                min_score (Integer)
                        Minimum score for calculating the p-value of scores (-M)

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/patser.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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