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


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


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

         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";


       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.



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


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       Donald Jackson (


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

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