Method: Bio::SiRNA#design

Defined in:
lib/bio/util/sirna.rb

#design(rule = 'uitei') ⇒ Object

rule can be one of ‘uitei’ (default) and ‘reynolds’.



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# File 'lib/bio/util/sirna.rb', line 105

def design(rule = 'uitei')
  @target_size = @antisense_size + 2

  target_start = 0
  @seq.window_search(@target_size) do |target|
    antisense = target.subseq(1, @target_size - 2).complement.rna
    sense     = target.subseq(3, @target_size)

    target_start += 1
    target_stop  = target_start + @target_size

    antisense_gc_percent = antisense.gc_percent
    next if antisense_gc_percent > @max_gc_percent
    next if antisense_gc_percent < @min_gc_percent
    
    case rule
    when 'uitei'
      next unless uitei?(target)
    when 'reynolds'
      next unless reynolds?(target)
    else
      raise NotImplementedError
    end

    pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
    @pairs.push(pair)
  end
  return @pairs
end