Bio::SeqFeature::SiRNA::Pair(3pm) User Contributed Perl Documentation Bio::SeqFeature::SiRNA::Pair(3pm)
NAME
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs
SYNOPSIS
use Bio::SeqFeature::SiRNA::Pair;
my $pair = Bio::SeqFeature::SiRNA::Pair->
new( -sense => $bio_seqfeature_sirna_oligo, # strand=1
-antisense => $bio_seqfeature_sirna_oligo, # strand= -1
-primary => 'SiRNA::Pair',
-source_tag => 'Bio::Tools::SiRNA',
-start => 8,
-end => 31,
-rank => 1,
-fxgc => 0.5,
-tag => { note => 'a note' } );
$target_sequence->add_SeqFeature($pair);
DESCRIPTION
Object methods for (complementary) pairs of Bio::SeqFeature::SiRNA::Oligo objects - inherits Bio::SeqFeature::Generic. See that package for
information on inherited methods.
Does not include methods for designing SiRNAs -- see Bio::Tools::SiRNA
SEE ALSO
Bio::SeqFeature::Oligo, Bio::Tools::SiRNA.
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 _
METHODS
new
Title : new
Usage : my $sirna_pair = Bio::SeqFeature::SiRNA::Pair->new();
Purpose : Create a new SiRNA::Pair object
Returns : Bio::Tools::SiRNA object
Args : -start 10
-end 31
-rank 1 # 'Rank' in Tuschl group's rules
-fxgc 0.5 # GC fraction for target sequence
-primary 'SiRNA::Pair', # default value
-source_tag 'Bio::Tools::SiRNA'
-tag { note => 'A note' }
-sense a Bio::SeqFeature::SiRNA::Oligo object
with strand = 1
-antisense a Bio::SeqFeature::SiRNA::Oligo object
with strand = -1
);
Note : SiRNA::Pair objects are typically created by a design
algorithm such as Bio::Tools::SiRNA
rank
Title : rank
Usage : my $pair_rank = $sirna_pair->rank()
Purpose : Get/set the 'quality rank' for this pair.
See Bio::Tools::SiRNA for a description of ranks.
Returns : scalar
Args : scalar (optional) indicating pair rank
fxGC
Title : fxGC
Usage : my $fxGC = $sirna_pair->fxGC();
Purpose : Get/set the fraction of GC for this pair - based on TARGET sequence, not oligos.
Returns : scalar between 0-1
Args : scalar between 0-1 (optional)
sense
Title : sense
Usage : my $sense_oligo = $sirna_pair->sense()
Purpose : Get/set the SiRNA::Oligo object corresponding to the sense strand
Returns : Bio::SeqFeature::SiRNA::Oligo object
Args : Bio::SeqFeature::SiRNA::Oligo object
antisense
Title : antisense
Usage : my $antisense_oligo = $sirna_pair->antisense()
Purpose : Get/set the SiRNA::Oligo object corresponding to the antisense strand
Returns : Bio::SeqFeature::SiRNA::Oligo object
Args : Bio::SeqFeature::SiRNA::Oligo object
perl v5.14.2 2012-03-02 Bio::SeqFeature::SiRNA::Pair(3pm)