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


       Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.


         use Bio::SeqFeature::SiRNA::Oligo;

         my $oligo = Bio::SeqFeature::SiRNA::Oligo->
             new( -seq         => 'AUGCCGAUUGCAAGUCAGATT',
                  -start       => 10,
                  -end         => 31,
                  -strand      => -1,
                  -primary     => 'SiRNA::Oligo',
                  -source_tag  => 'Bio::Tools::SiRNA',
                  -tag         => { note => 'A note' }, );

         # normally two complementary Oligos are combined in an SiRNA::Pair
         # object


       Object methods for single SiRNA oligos - inherits Bio::SeqFeature::Generic.  Does not
       include methods for designing SiRNAs - see Bio::Tools::SiRNA for that.


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


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

         Title         : new
         Usage         : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new();
         Function      : Create a new SiRNA::Oligo object
         Returns       : Bio::Tools::SiRNA object
         Args          : -seq            sequence of the RNAi oligo.  Should be in RNA alphabet
                                         except for the final TT overhang.
                         -start          start position
                         -end            end position
                         -strand         strand
                         -primary        primary tag - defaults to 'SiRNA::Oligo'
                         -source         source tag
                         -score          score value
                         -tag            a reference to a tag/value hash
                         -seq_id         the display name of the sequence
                         -annotation     the AnnotationCollectionI object
                         -location       the LocationI object

       Currently passing arguments in gff_string or gff1_string is not supported.  SiRNA::Oligo
       objects are typically created by a design algorithm such as Bio::Tools::SiRNA

         Title         : Seq
         Usage         : my $oligo_sequence = $sirna_oligo->seq();
         Purpose       : Get/set the sequence of the RNAi oligo
         Returns       : Sequence for the RNAi oligo
         Args          : Sequence of the RNAi oligo (optional)
         Note          : Overloads Bio::SeqFeature::Generic seq method - the oligo and
                         parent sequences are different.
                         Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
                         SiRNA::Pair objects are typically created by a design algorithm such as