NAME

Bio::Tools::Run::PiseApplication::nrscope

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::nrscope

      Bioperl class for:

        NRSCOPE Converts redundant EMBL-format SCOP file to non-redundant one (EMBOSS)


      Parameters: 

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


                nrscope (String)

                init (String)

                scopin (InFile)
                        Name of scop file for input (embl-like format) (-scopin)

                dpdb (String)
                        Location of clean domain coordinate files for input (embl-like format) (-dpdb)

                extn (String)
                        File extension of clean domain coordinate files (-extn)

                thresh (Float)
                        The % sequence identity redundancy threshold (-thresh)

                datafile (Excl)
                        Residue substitution matrix (-datafile)

                gapopen (Float)
                        Gap insertion penalty (-gapopen)

                gapextend (Float)
                        Gap extension penalty (-gapextend)

                scopout (OutFile)
                        Name of non-redundant scop file for output (embl-like format) (-scopout)

                errf (OutFile)
                        Name of log file for the build (-errf)

                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/nrscope.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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