NAME

Bio::Tools::Run::PiseApplication::palindrome

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::palindrome

      Bioperl class for:

        PALINDROME      Looks for inverted repeats in a nucleotide sequence (EMBOSS)


      Parameters: 

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


                palindrome (String)

                init (String)

                insequence (Sequence)
                        insequence -- nucleotide [sequences] (-insequence)
                        pipe: seqsfile

                minpallen (Integer)
                        Enter minimum length of palindrome (-minpallen)

                maxpallen (Integer)
                        Enter maximum length of palindrome (-maxpallen)

                gaplimit (Integer)
                        Enter maximum gap between repeated regions (-gaplimit)

                nummismatches (Integer)
                        Number of mismatches allowed (-nummismatches)

                outfile (OutFile)
                        outfile (-outfile)

                overlap (Switch)
                        Report overlapping matches (-overlap)

                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/palindrome.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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