Bio::Tools::Run::PiseApplication::pima(3)

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/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/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.