NAME

Bio::Tools::Run::PiseApplication::siggen

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::siggen

      Bioperl class for:

        SIGGEN  Generates a sparse protein signature (EMBOSS)


      Parameters: 

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


                siggen (String)

                init (String)

                algpath (InFile)
                        Location of alignment files for input (-algpath)

                algextn (String)
                        Extension of alignment files for input (-algextn)

                sparsity (Integer)
                        % sparsity of signature (-sparsity)

                randomise (Switch)
                        Generate a randomised signature (-randomise)

                seqoption (List)
                        Select number -- Sequence variability scoring method [select  values] (-seqoption)

                datafile (Excl)
                        Substitution matrix to be used (-datafile)

                conoption (List)
                        Select number -- Residue contacts scoring method [select  values] (-conoption)

                filtercon (Switch)
                        Ignore alignment positions making less than a threshold number of contacts (-filtercon)

                conthresh (Integer)
                        Threshold contact number (-conthresh)

                conpath (String)
                        Location of contact files for input (-conpath)

                conextn (String)
                        Extension of contact files (-conextn)

                cpdbpath (String)
                        Location of coordinate files for input (embl-like format) (-cpdbpath)

                cpdbextn (String)
                        Extension of coordinate files (embl-like format) (-cpdbextn)

                filterpsim (Switch)
                        Ignore alignment postitions with post_similar value of 0 (-filterpsim)

                sigextn (String)
                        Extension of signature files for output (-sigextn)

                auto (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/siggen.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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