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
FEEDBACK
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AUTHOR
Donald Jackson ([email protected])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