Bio::Tools::Run::PiseApplication::scan_for_matches.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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/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 (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.