NAME

Bio::Tools::Run::PiseApplication::pima

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::pima

      Bioperl class for:

        PIMA    Pattern-Induced Multi-sequence Alignment program (R. D. Smith and T. F. Smith)

        References:

                R. D. Smith and T. F. Smith. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative modelling. protein Engineering, vol5, number 1, pp 35-41, 1992



      Parameters: 

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


                pima (String)

                sequence (Sequence)
                        Sequences

                cluster_name (String)
                        cluster_name

                ref_seq_name (String)
                        ref_seq_name

                sec_struc_seq_filename (InFile)
                        sec_struc_seq_filename

                score_cutoff (Float)
                         cluster score cutoff (-c) 

                ext_gap_cost (Integer)
                         gap extension penalty (-d) 

                gap_open_cost (Integer)
                         gap opening penalty (-i) 

                min_score (Integer)
                         minimum local score (-l) 

                mat_file (InFile)
                         matrix file (-m) 

                not_num_ext (Switch)
                        Do not use numerical extensions on each step of the alignment. (-n)

                sec_struc_gap_cost (Integer)
                        secondary structure gap penalty (-t)

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/pima.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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