NAME

Bio::Tools::Run::PiseApplication::plsearch

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::plsearch

      Bioperl class for:

        PLSEARCH        search protein sequences for similarity to AACC patterns (R. Smith & T. Smit)

        References:

                Smith, Randall F. and Temple F. Smith (1990).  Automatic generation of diagnostic sequence patterns from sets of related protein sequences.  Proc. Natl. Acad. Sci. USA 87:118-122.



      Parameters: 

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


                plsearch (String)

                type (String)

                no_detach (String)

                protein (Sequence)
                        Protein sequence File

                outfile (OutFile)
                        Results file

                max_alignements (Integer)
                        Maximum number of alignments

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/plsearch.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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