NAME

Bio::Tools::Run::PiseApplication::scan_for_matches

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::scan_for_matches

      Bioperl class for:

        scan_for_matches        Scan Nucleotide or Protein Sequences for Matching Patterns


      Parameters: 

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


                scan_for_matches (String)

                sequence (Sequence)
                        Input sequence

                pattern (String)
                        Search pattern

                mismatches (Integer)
                        Number of mismatches

                deletions (Integer)
                        Number of deletions

                insertions (Integer)
                        Number of insertions

                info_user_pattern_file (Label)
                        Please look at the documentation for using your own patterns.

                user_pattern_file (InFile)
                        You may give your own patterns

                complementary_strand (Switch)
                        Search complementary strand

                protein (Switch)
                        Protein

                stop_after_n_misses (Integer)
                        Stop after n misses

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/scan_for_matches.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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