Provided by: libbio-perl-perl_1.6.901-2_all bug

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 ("\t", $pair->start, $pair->end, $pair->rank,
                         $sense_oligo_sequence, $antisense_oligo_sequence), "\n";
         }

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