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://github.com/bioperl/bioperl-live/issues
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