Bio::SeqFeature::SiRNA::Oligo(3pm) User Contributed Perl Documentation Bio::SeqFeature::SiRNA::Oligo(3pm)
NAME
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
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.
SEE ALSO
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.
FEEDBACK
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/wiki/Mailing_lists - About the mailing lists
Support
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 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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Donald Jackson (donald.jackson@bms.com)
APPENDIX
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.
perl v5.14.2 2012-03-02 Bio::SeqFeature::SiRNA::Oligo(3pm)