# sirna.rb

Path: | lib/bio/util/sirna.rb
Last Update: | Mon Nov 29 07:49:59 +0000 2010

# bio/util/sirna.rb - Class for designing small inhibitory RNAs

Copyright: | Copyright (C) 2004, 2005 Itoshi NIKAIDO <dritoshi@gmail.com>
License: | The Ruby License

$Id:$

## Bio::SiRNA - Designing siRNA.

This class implements the selection rules described by Kumiko Ui-Tei et al. (2004) and Reynolds et al. (2004).

## Example

     seq = Bio::Sequence::NA.new(ARGF.read)

     sirna = Bio::SiRNA.new(seq)
     pairs = sirna.design

     pairs.each do |pair|
       puts pair.report
       shrna = Bio::SiRNA::ShRNA.new(pair)
       shrna.design
       puts shrna.report

       puts shrna.top_strand.dna
       puts shrna.bottom_strand.dna
     end

## References

- Kumiko Ui-Tei et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucl. Acids. Res. 2004 32: 936-948.
- Angela Reynolds et al. Rational siRNA design for RNA interference. Nature Biotech. 2004 22: 326-330.

### Required files

bio/sequence

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