| Bio::SeqFeature::SiRNA::Oligo(3pm) | User Contributed Perl Documentation | Bio::SeqFeature::SiRNA::Oligo(3pm) |
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.
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.
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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Please direct usage questions or support issues to the mailing list:
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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.
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:
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Donald Jackson (donald.jackson@bms.com)
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
Bio::Tools::SiRNA.
| 2018-10-27 | perl v5.26.2 |