NAME

Bio::Tools::Run::PiseApplication::sirna

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::sirna

      Bioperl class for:

        SIRNA   Finds siRNA duplexes in mRNA (EMBOSS)


      Parameters: 

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


                sirna (String)

                init (String)

                sequence (Sequence)
                        sequence -- DNA [sequences] (-sequence)
                        pipe: seqsfile

                poliii (Switch)
                        Select probes for Pol III expression vectors (-poliii)

                aa (Switch)
                        Select only regions that start with AA (-aa)

                tt (Switch)
                        Select only regions that end with TT (-tt)

                polybase (Switch)
                        Allow regions with 4 repeats of a base (-polybase)

                outfile (OutFile)
                        Output data file (-outfile)

                outseq (OutFile)
                        Output sequence file (-outseq)
                        pipe: seqsfile

                outseq_sformat (Excl)
                        Output format for: Output sequence file

                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/sirna.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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