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

NAME

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

SYNOPSIS

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

	 use Bio::Tools::SiRNA;

	 my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
						      -rules  => 'saigo'
	   );
	 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 published by Ui-Tei et al(2004).  The rules are:

       1.   The first base in the sense strand of the duplex must be a G or C

       2.   The first base in the antisense strand of the duplex must be an A or U

       3.   The first 7 nucleotides in the antisense strand of the duplex must be A or U

       4.   There cannot be more than 9 consecutive G or C nucleotides

       5.   The first 12 nucleotides in the sense strand of the duplex should have 33-66% GC

       The module inherits from Bio::Tools::SiRNA.  See the documentation for that module for information on how to specify the target and recover
       the SiRNA duplex information.

   EXPORT
       None.

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::saigo(3pm)