NAME

Bio::Tools::Run::PiseApplication::lassap

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::lassap

      Bioperl class for:

        LASSAP  LArge Scale Sequence compArison Package (Glemet, Codani)


      Parameters: 

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


                lassap (String)

                method (Excl)
                        Comparison method

                dna_comp (Switch)
                        nucleic/nucleic comparison

                query1 (Sequence)
                        First sequence

                query2 (Sequence)
                        Second sequence

                dr1 (String)

                dr2 (String)

                matrix (Excl)
                        Scoring matrix

                gapo (Integer)
                        Gap open penalty

                gape (Integer)
                        Gap extension penalty

                cutoff (Integer)
                        Cutoff

                Expect (Integer)
                        Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (E)

                E2 (Integer)
                        E2 (expected number of HSPs that will be found when comparing two sequences that each have the same length)

                S2 (Integer)
                        S2 (cutoff score which defines HSPs)

                W (Integer)
                        W (length of words identified in the query sequence)

                T (Integer)
                        T (neighborhood word score threshold)

                X (Integer)
                        X (word hit extension drop-off score)

                ktup (Integer)
                        ktup : sensitivity and speed of the search

                init1 (Switch)
                        sequences ranked by the z-score based on the init1 score

                noopt (Switch)
                        no limited optimization

                linlen (Integer)
                        output line length for sequence alignments (< 200)

                ran (Integer)
                        How many randomizations

                swap (Switch)
                        Don't test for inclusion of query1 into query2

                k (Integer)
                        How many best alignments

                frame_query1 (List)
                        First sequence frames

                frame_query2 (List)
                        Second sequence frames

                gc (Excl)
                        Genetic Code

                view_alignment (Switch)
                        View alignment (not available for all methods)

                scut (Integer)
                        Score cutoff

                pcut (Integer)
                        Probability cutoff

                max (Integer)
                        Maximum retained

                flag_algo_opt (String)

                flag_algo_opt2 (String)

                gc2 (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

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/lassap.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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