Provided by: libbio-perl-perl_1.6.924-3_all bug

NAME

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

SYNOPSIS

         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
         $pair->antisense($oligo);

DESCRIPTION

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

SEE ALSO

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

FEEDBACK

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       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://github.com/bioperl/bioperl-live/issues

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         : 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

   seq
         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
                         Bio::Tools::SiRNA.