Bio::SeqFeature::SiRNA Oligo
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Summary
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
Package variables
No package variables defined.
Inherit
Bio::SeqFeature::Generic
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.
Methods
newDescriptionCode
seqDescriptionCode
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
seqcodeprevnextTop
  Title		: Seq
Usage : my $oligo_sequence = $sirna_oligo->seq();
Purpose : Get/set the sequence of the RNAi oligo
Returns : Sequence for the RNAi oligo
Args : Sequence of the RNAi oligo (optional)
Note : Overloads Bio::SeqFeature::Generic seq method - the oligo and
parent sequences are different.
Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
SiRNA::Pair objects are typically created by a design algorithm such as
Bio::Tools::SiRNA.
Methods code
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
seqdescriptionprevnextTop
sub seq {
    my ($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
SEE ALSOTop
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.
FEEDBACKTop
Mailing ListsTop
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.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Donald Jackson (donald.jackson@bms.com)
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _