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

EXPORT
None by default. Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair, perl.

Mailing Lists
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/MailList.shtml - About the mailing lists

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: 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 _

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.