sirna.rb

Path: lib/bio/util/sirna.rb
Last Update: Sun Dec 04 02:16:41 +0000 2011

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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