---
name: "Bio::SeqFeature::SiRNA::Pair"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::SeqFeature::SiRNA::Pair"
---

# Bio::SeqFeature::SiRNA::Pair(3pm)

Perl object for small inhibitory RNA (SiRNA) oligo pairs

## 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
```