# File lib/bio/util/sirna.rb
66 def initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0)
67   @seq = seq.rna!
68   @pairs = Array.new
69   @antisense_size = antisense_size
70   @max_gc_percent = max_gc_percent
71   @min_gc_percent = min_gc_percent
72 end

    # File lib/bio/util/sirna.rb
147 def design(rule = 'uitei')
148   @target_size = @antisense_size + 2
149 
150   target_start = 0
151   @seq.window_search(@target_size) do |target|
152     antisense = target.subseq(1, @target_size - 2).complement.rna
153     sense     = target.subseq(3, @target_size)
154 
155     target_start += 1
156     target_stop  = target_start + @target_size
157 
158     antisense_gc_percent = antisense.gc_percent
159     next if antisense_gc_percent > @max_gc_percent
160     next if antisense_gc_percent < @min_gc_percent
161     
162     case rule
163     when 'uitei'
164       next unless uitei?(target)
165     when 'reynolds'
166       next unless reynolds?(target)
167     else
168       raise NotImplementedError
169     end
170 
171     pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
172     @pairs.push(pair)
173   end
174   return @pairs
175 end

    # File lib/bio/util/sirna.rb
142 def reynolds
143   design('reynolds')
144 end

    # File lib/bio/util/sirna.rb
 97 def reynolds?(target)
 98   return false if target.length != 23  # 21 nt target + 2 nt overhang
 99 
100   seq19 = target[2..20]  # 19 nt double-stranded region of siRNA
101   score = 0
102 
103   # criteria I
104   gc_number = seq19.scan(/[GC]/i).size
105   score += 1 if (7 <= gc_number and gc_number <= 10)
106 
107   # criteria II
108   au_number = seq19[14..18].scan(/[AU]/i).size
109   score += au_number
110 
111   # criteria III
112   # NotImpremented: Tm
113 
114   # criteria IV
115   score += 1 if seq19[18..18].match(/A/i)
116 
117   # criteria V
118   score += 1 if seq19[2..2].match(/A/i)
119 
120   # criteria VI
121   score += 1 if seq19[9..9].match(/[U]/i)
122 
123   # criteria VII
124   score -= 1 if seq19[18..18].match(/[GC]/i)
125 
126   # criteria VIII
127   score -= 1 if seq19[12..12].match(/G/i)
128 
129   if score >= 6
130     return score
131   else
132     return false
133   end
134 end

    # File lib/bio/util/sirna.rb
137 def uitei
138   design('uitei')
139 end

   # File lib/bio/util/sirna.rb
75 def uitei?(target)
76   return false if target.length != 23  # 21 nt target + 2 nt overhang
77 
78   seq19 = target[2..20]  # 19 nt double-stranded region of siRNA
79 
80   # criteria i
81   return false unless seq19[18..18].match(/[AU]/i)
82 
83   # criteria ii
84   return false unless seq19[0..0].match(/[GC]/i)
85 
86   # criteria iii
87   au_number = seq19[12..18].scan(/[AU]/i).size
88   return false unless au_number >= 4
89 
90   # criteria iv
91   return false if seq19.match(/[GC]{10}/i)
92 
93   return true
94 end