NAME

Bio::Tools::Run::PiseApplication::align2model

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::align2model

      Bioperl class for:

        SAM     align2model - create a multiple alignment of sequences to an existing model (R. Hughey, A. Krogh)

        References:

                R. Hughey and A. Krogh., SAM: Sequence alignment and modeling software system. Technical Report UCSC-CRL-96-22, University of California, Santa Cruz, CA, September 1996. 



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/align2model.html 
         for available values):


                align2model (String)

                run (String)
                        Run name

                db (Sequence)
                        Sequences to align (-db)

                model_file (InFile)
                        Model (-i)
                        pipe: sam_model

                id (String)
                        Sequence identifier(s) selection (separated by commas) (-id)

                nscoreseq (Integer)
                        Maximum number of sequences to be read (-nscoreseq)

                adpstyle (Excl)
                        Dynamic programming style (-adpstyle

                SW (Excl)
                        Sequence scoring (-SW)

                auto_fim (Switch)
                        Add FIMs automatically (-auto_fim)

                jump_in_prob (Float)
                        Probability cost of jumping into the center of the model (-jump_in_prob)

                jump_out_prob (Float)
                        Probability cost of jumping out the center of the model (-jump_out_prob)

                a2mdots (Switch)
                        Print dots to fill space need for other sequences' insertions (-a2mdots)

                dump_parameters (Excl)
                        (-dump_parameters)

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/align2model.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $align2model = Bio::Tools::Run::PiseApplication::align2model->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::align2model 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 $align2model = $factory->program('align2model');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::align2model.