Class: Bio::SiRNA
Overview
Bio::SiRNA
Designing siRNA.
This class implements the selection rules described by Kumiko Ui-Tei et al. (2004) and Reynolds et al. (2004).
Defined Under Namespace
Instance Attribute Summary collapse
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#antisense_size ⇒ Object
A parameter of size of antisense.
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#max_gc_percent ⇒ Object
A parameter of maximal %GC.
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#min_gc_percent ⇒ Object
A parameter of minimum %GC.
Instance Method Summary collapse
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#design(rule = 'uitei') ⇒ Object
rule can be one of ‘uitei’ (default) and ‘reynolds’.
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#initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0) ⇒ SiRNA
constructor
Input is a Bio::Sequence::NA object (the target sequence).
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#reynolds ⇒ Object
same as design(‘reynolds’).
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#reynolds?(target) ⇒ Boolean
Reynolds’ rule.
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#uitei ⇒ Object
same as design(‘uitei’).
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#uitei?(target) ⇒ Boolean
Ui-Tei’s rule.
Constructor Details
#initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0) ⇒ SiRNA
Input is a Bio::Sequence::NA object (the target sequence). Output is a list of Bio::SiRNA::Pair object.
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# File 'lib/bio/util/sirna.rb', line 65 def initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0) @seq = seq.rna! @pairs = Array.new @antisense_size = antisense_size @max_gc_percent = max_gc_percent @min_gc_percent = min_gc_percent end |
Instance Attribute Details
#antisense_size ⇒ Object
A parameter of size of antisense.
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# File 'lib/bio/util/sirna.rb', line 55 def antisense_size @antisense_size end |
#max_gc_percent ⇒ Object
A parameter of maximal %GC.
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# File 'lib/bio/util/sirna.rb', line 58 def max_gc_percent @max_gc_percent end |
#min_gc_percent ⇒ Object
A parameter of minimum %GC.
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# File 'lib/bio/util/sirna.rb', line 61 def min_gc_percent @min_gc_percent end |
Instance Method Details
#design(rule = 'uitei') ⇒ Object
rule can be one of ‘uitei’ (default) and ‘reynolds’.
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# File 'lib/bio/util/sirna.rb', line 146 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 |
#reynolds ⇒ Object
same as design(‘reynolds’).
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# File 'lib/bio/util/sirna.rb', line 141 def reynolds design('reynolds') end |
#reynolds?(target) ⇒ Boolean
Reynolds’ rule.
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# File 'lib/bio/util/sirna.rb', line 96 def reynolds?(target) return false if target.length != 23 # 21 nt target + 2 nt overhang seq19 = target[2..20] # 19 nt double-stranded region of siRNA score = 0 # criteria I gc_number = seq19.scan(/[GC]/i).size score += 1 if (7 <= gc_number and gc_number <= 10) # criteria II au_number = seq19[14..18].scan(/[AU]/i).size score += au_number # criteria III # NotImpremented: Tm # criteria IV score += 1 if seq19[18..18].match(/A/i) # criteria V score += 1 if seq19[2..2].match(/A/i) # criteria VI score += 1 if seq19[9..9].match(/[U]/i) # criteria VII score -= 1 if seq19[18..18].match(/[GC]/i) # criteria VIII score -= 1 if seq19[12..12].match(/G/i) if score >= 6 return score else return false end end |
#uitei ⇒ Object
same as design(‘uitei’).
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# File 'lib/bio/util/sirna.rb', line 136 def uitei design('uitei') end |
#uitei?(target) ⇒ Boolean
Ui-Tei’s rule.
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# File 'lib/bio/util/sirna.rb', line 74 def uitei?(target) return false if target.length != 23 # 21 nt target + 2 nt overhang seq19 = target[2..20] # 19 nt double-stranded region of siRNA # criteria i return false unless seq19[18..18].match(/[AU]/i) # criteria ii return false unless seq19[0..0].match(/[GC]/i) # criteria iii au_number = seq19[12..18].scan(/[AU]/i).size return false unless au_number >= 4 # criteria iv return false if seq19.match(/[GC]{10}/i) return true end |