NAME

Bio::Tools::Run::PiseApplication::sigscan

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::sigscan

      Bioperl class for:

        SIGSCAN Scans a sparse protein signature against swissprot (EMBOSS)


      Parameters: 

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


                sigscan (String)

                init (String)

                sigin (InFile)
                        Name of signature file for input (-sigin)

                database (Sequence)
                        Name of sequence database to search (-database)
                        pipe: seqsfile

                targetf (InFile)
                        Name of (optionally grouped) scop families file for input (-targetf)

                thresh (Integer)
                        Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit. (-thresh)

                sub (Excl)
                        Residue substitution matrix (-sub)

                gapo (Float)
                        Gap insertion penalty (-gapo)

                gape (Float)
                        Gap extension penalty (-gape)

                nterm (Excl)
                        Select number -- N-terminal matching options (-nterm)

                nhits (Integer)
                        Number of hits to output (-nhits)

                hitsf (OutFile)
                        Name of signature hits file for output (-hitsf)

                alignf (OutFile)
                        Name of signature alignments file for output (-alignf)

                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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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/sigscan.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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