# File lib/bio/util/sirna.rb
235 def initialize(pair)
236   @pair = pair
237 end

    # File lib/bio/util/sirna.rb
252 def block_it(method = 'piGENE')
253   top = Bio::Sequence::NA.new('CACC') # top_strand_shrna_overhang
254   bot = Bio::Sequence::NA.new('AAAA') # bottom_strand_shrna_overhang
255   fwd = @pair.sense
256   rev = @pair.sense.complement
257 
258   case method
259   when 'BLOCK-iT'
260     # From BLOCK-iT's manual
261     loop_fwd = Bio::Sequence::NA.new('CGAA')
262     loop_rev = loop_fwd.complement
263   when 'piGENE'
264     # From piGENE document
265     loop_fwd = Bio::Sequence::NA.new('GTGTGCTGTCC')
266     loop_rev = loop_fwd.complement
267   else
268     raise NotImplementedError
269   end
270 
271   if /^G/i =~ fwd
272     @top_strand    = top + fwd + loop_fwd + rev
273     @bottom_strand = bot + fwd + loop_rev + rev
274   else
275     @top_strand    = top + 'G' + fwd + loop_fwd + rev
276     @bottom_strand = bot + fwd + loop_rev + rev + 'C'
277   end
278 end

    # File lib/bio/util/sirna.rb
240 def design(method = 'BLOCK-iT')
241   case method
242   when 'BLOCK-iT'
243     block_it
244   else
245     raise NotImplementedError
246   end
247 end

    # File lib/bio/util/sirna.rb
281 def report
282   # raise NomethodError for compatibility
283   raise NoMethodError if !defined?(@top_strand) || !@top_strand
284   report = "### shRNA\n".dup
285   report << "Top strand shRNA (#{@top_strand.length} nt):\n"
286   report << "  5'-#{@top_strand.upcase}-3'\n"
287   report << "Bottom strand shRNA (#{@bottom_strand.length} nt):\n"
288   report << "      3'-#{@bottom_strand.reverse.upcase}-5'\n"
289 end