Bio::SeqFeature::SiRNA Oligo
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
Package variables
No package variables defined.
  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);
Object methods for single SiRNA oligos - inherits
Bio::SeqFeature::Generic. Does not include methods for designing
SiRNAs - see Bio::Tools::SiRNA for that.
Methods description
newcode    nextTop
  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 = $sirna_oligo->seq();
Purpose : Get/set the sequence of the RNAi oligo
Returns : Sequence for the RNAi oligo
Args : Sequence of the RNAi oligo (optional)
Note : Overloads Bio::SeqFeature::Generic seq method - the oligo and
parent sequences are different.
Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
SiRNA::Pair objects are typically created by a design algorithm such as
Methods code
sub new {
    my ($proto, @args) = @_;

    my $pkg = ref($proto) || $proto;

    my (%args);

    my $self = $pkg->SUPER::new();

    @args{@ARGNAMES} = $self->_rearrange(\@ARGNAMES, @args); 
    # default primary tag
$args{'PRIMARY'} ||= 'SiRNA::Oligo'; $args{'PRIMARY'} && $self->primary_tag($args{'PRIMARY'}); $args{'SOURCE_TAG'} && $self->source_tag($args{'SOURCE_TAG'}); $args{'SEQNAME'} && $self->seqname($args{'SEQNAME'}); $args{'SEQ'} && $self->seq($args{'SEQ'}); $args{'ANNOTATION'} && $self->annotation($args{'ANNOTATION'}); $args{'LOCATION'} && $self->location($args{'LOCATION'}); defined($args{'START'}) && $self->start($args{'START'}); defined($args{'END'}) && $self->end($args{'END'}); defined($args{'STRAND'}) && $self->strand($args{'STRAND'}); defined($args{'SCORE'}) && $self->score($args{'SCORE'}); if ($args{'TAG'}) { foreach my $t ( keys %{ $args{'TAG'} } ) { $self->add_tag_value($t, $args{'TAG'}->{$t}); } } return $self;
sub seq {
    my ($self, $seq) = @_;
    if ($seq) {
	# check alphabet
if ($seq =~ /[^ACGTUacgtu]/ ) { warn "Sequence contains illegal characters"; return; } else { $self->{'seq'} = $seq; } } return $self->{'seq'}; } 1;
General documentation
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 _