Summary

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

Package variables

Included modules

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. None by default.

Methods

Methods description

  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

  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.

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 undef;
	}
	else {
	    $self->{'seq'} = $seq;
	}
    }
    return $self->{'seq'};

}

General documentation

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

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

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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:

  http://bugzilla.bioperl.org/

Donald Jackson (donald.jackson@bms.com)

Additional contributors names and emails here

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