Bio::SeqFeature::SiRNA::Oligo(3) Perl object for small inhibitory RNAs.


use Bio::SeqFeature::SiRNA::Oligo;
my $oligo = Bio::SeqFeature::SiRNA::Oligo->
-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.


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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