NAME

Bio::Tools::Run::PiseApplication::pestfind

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::pestfind

      Bioperl class for:

        PESTFIND        Finds PEST motifs as potential proteolytic cleavage sites (EMBOSS)


      Parameters: 

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


                pestfind (String)

                init (String)

                sequence (Sequence)
                        Enter input sequence (-sequence)
                        pipe: seqfile

                window (Integer)
                        Enter window length (-window)

                order (Excl)
                        Select sort order of results -- Sort order of results (-order)

                potential (Switch)
                        Display potential PEST motifs (-potential)

                poor (Switch)
                        Display poor PEST motifs (-poor)

                invalid (Switch)
                        Display invalid PEST motifs (-invalid)

                map (Switch)
                        Display PEST motifs map (-map)

                outfile (OutFile)
                        Enter output filename (-outfile)

                graph (Excl)
                        graph (-graph)

                threshold (Float)
                        Enter threshold score (-threshold)

                aadata (String)
                        Enter amino acid data filename (-aadata)

                auto (String)

                psouput (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/pestfind.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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