| Bio::SeqFeature::SiRNA::Pair(3pm) | User Contributed Perl Documentation | Bio::SeqFeature::SiRNA::Pair(3pm) |
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs
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);
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
Bio::SeqFeature::Oligo, Bio::Tools::SiRNA.
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
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.
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
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_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
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
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)
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
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
| 2018-10-27 | perl v5.26.2 |