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