Last Modified
2013-06-13 00:59:09 +0000
Requires
  • bio/sequence

Description

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