NAME

Bio::Tools::Run::PiseApplication::blimps

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::blimps

      Bioperl class for:

        BLIMPS  BLocks IMProved Searcher (Wallace, Henikoff)


      Parameters: 

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


                blimps (String)

                action (Excl)
                        Action

                blocks_db (Excl)
                        Blocks database

                sequence_file (Sequence)
                        Sequence file filename to score against blocks database

                sequence_db (Excl)
                        Sequences database

                block_file (InFile)
                        Block file filename

                matrix_file (InFile)
                        A precomputed site specific scoring matrix file

                conversion (Excl)
                        Conversion method for converting a block to a matrix

                genetic_code (Excl)
                        The Genetic code to use

                strand (Switch)
                        both strands to be searched

                outfile (OutFile)
                        Output file filename

                error (Excl)
                        Error level to report at

                export_matrix (OutFile)
                        Export matrix (matricies) to this filename

                histogram (Switch)
                        Print the histogram values in the output file

                scores_number (Integer)
                        The number of scores to report.

                repeats (Switch)
                        Repeats are allowed in the scoring list

                error_file (OutFile)

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/blimps.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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