debian man page for bio::tools::sirna::ruleset::tuschl

Bio::Tools::SiRNA::Ruleset::tuschl(3pm) 		User Contributed Perl Documentation		   Bio::Tools::SiRNA::Ruleset::tuschl(3pm)

NAME
       Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs

SYNOPSIS
       Do not use this module directly.  Instead, use Bio::Tools::SiRNA and specify the tuschl ruleset:

	 use Bio::Tools::SiRNA;

	 my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
						      -rules  => 'tuschl'
	   );
	 my @pairs = $sirna_designer->design;

	 foreach $pair (@pairs) {
	     my $sense_oligo_sequence = $pair->sense->seq;
	     my $antisense_oligo_sequence = $pair->antisense->seq;

	     # print out results
	     print join ("	", $pair->start, $pair->end, $pair->rank,
			 $sense_oligo_sequence, $antisense_oligo_sequence), "
";
	 }

DESCRIPTION
       This package implements the rules for designing siRNA reagents developed by Tuschl and colleagues (see
       http://www.rockefeller.edu/labheads/tuschl/sirna.html). It looks for oligos that match the following patterns in the target sequence:

	 1. AA(N19)TT (rank 1)
	 2. AA(N21) (rank 2)
	 3. NA(N21) (rank 3)

       The package also supports selection of siRNA seqences that can be transcribed by pol3:

	   A[A,G]N17[C,T]

SEE ALSO
       Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair, Bio::SeqFeature::SiRNA::Oligo.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR
       Donald Jackson (donald.jackson@bms.com)

APPENDIX
       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	 Title : new
	 Usage : Do not call directly - use Bio::Tools::SiRNA->new instead.
	 Returns : Bio::Tools::SiRNA::Ruleset::saigo object
	 Args  : none

perl v5.14.2							    2012-03-02				   Bio::Tools::SiRNA::Ruleset::tuschl(3pm)