Provided by: libbio-perl-perl_1.7.2-3_all bug


       SiRNA - Perl object for designing small inhibitory RNAs.


         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";


       Package for designing siRNA reagents.

       Input is a Bio::SeqI-compliant object (the target).

       Output is a list of Bio::SeqFeature::SiRNA::Pair objects, which are added to the feature
       table of the target sequence.  Each Bio::SeqFeature::SiRNA::Pair contains two subfeatures
       (Bio::SeqFeature::Oligo objects) which correspond to the individual oligos.  These objects
       provide accessors for the information on the individual reagent pairs.

       This version of Bio::Tools::SiRNA represents a major change in architecture.  Specific
       'rulesets' for siRNA selection as developed by various groups are implemented as
       Bio::Tools::SiRNA::Ruleset objects, which inherit from Bio::Tools::SiRNA.  This will make
       it easier to add new rule sets or modify existing approaches. Currently the Tuschl and Ui-
       Tei (2004) rules are implemented. For consistency, the Tuschl rules are implemented by

       In addition, this module provides three 'extra' rules which can be added above and beyond
       any ruleset.

       1. SiRNAs that overlap known SNPs (identified as SeqFeatures with primary tag = variation)
          can be avoided.

       2. Other regions (with primary tag = 'Excluded') can also be skipped.  I use this with
          Bio::Tools::Run::Mdust to avoid low-complexity regions (must be run separately), but
          other programs could also be used.

       3. SiRNAs may also be selected in the 3 prime UTR of a gene by setting
          $sirna_designer->include_3pr() to true.



       Bio::Tools::Run::Mdust, 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          : my $sirna_designer = Bio::Tools::SiRNA->new();
        Function       : Constructor for designer object
        Returns        : Bio::Tools::SiRNA object
        Args           : target - the target sequence for the SiRNAs as a Bio::Seq::RichSeq
                         start_pad - distance from the CDS start to skip (default 75)
                         end_pad - distance from the CDS end to skip (default 50)
                         include_3pr - set to true to include SiRNAs in the 3prime UTR (default false)
                         rules - rules for selecting siRNAs, currently supporting saigo and tuschl
                         min_gc - minimum GC fraction (NOT percent) (default 0.4)
                         max_gc - maximum GC fraction (NOT percent) (default 0.6)
                         cutoff - worst 'rank' accepted(default 3)
                         avoid_snps - boolean - reject oligos that overlap a variation
                            SeqFeature in the target (default true)
                         gstring - maximum allowed consecutive Gs.
                            Too many can cause problems in synthesis (default 4)
         Note          : All arguments can also be changed/accessed using autoloaded
                        methods such as:

           my $start_pad = $sirna_designer->start_pad().

         Title         : target
         Usage         : my $target_seq = $sirna_designer->target(); # get the current target
                         $sirna_designer->target($new_target_seq); # set a new target
         Function      : Set/get the target as a Bio::SeqI-compliant object
         Returns       : a Bio::SeqI-compliant object
         Args          : a Bio::SeqI-compliant object (optional)

           Title       : rules
           Usage       : $sirna->rules('ruleset')
           Purpose     : set/get ruleset to use for selecting SiRNA oligo pairs.
           Returns     : not sure yet
           Args        : a ruleset name (currently supported: Tuschl, Saigo)
                         or a Bio::Tools::SiRNA::RulesetI compliant object

         Title         : design
         Usage         : my @pairs = $sirna_designer->design();
         Purpose       : Design SiRNA oligo pairs.
         Returns       : A list of SiRNA pairs as Bio::SeqFeature::SiRNA::Pair objects
         Args          : none

         Title         : add_oligos
         Usage         : $sirna_designer->add_oligos($sequence, $start, $rank);
         Purpose       : Add SiRNA olgos to target Bio::Seq as Bio::SeqFeature::SiRNA::Pair objects
         Args          : Oligo sequence and start position (required), rank/score (optional)