Class Bio::SiRNA
In: lib/bio/util/sirna.rb
Parent: Object

Bio::SiRNA

Designing siRNA.

This class implements the selection rules described by Kumiko Ui-Tei et al. (2004) and Reynolds et al. (2004).

Methods

design   new   reynolds   reynolds?   uitei   uitei?  

Classes and Modules

Class Bio::SiRNA::Pair
Class Bio::SiRNA::ShRNA

Attributes

antisense_size  [RW]  A parameter of size of antisense.
max_gc_percent  [RW]  A parameter of maximal %GC.
min_gc_percent  [RW]  A parameter of minimum %GC.

Public Class methods

new(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0)

Input is a Bio::Sequence::NA object (the target sequence). Output is a list of Bio::SiRNA::Pair object.

[Source]

    # File lib/bio/util/sirna.rb, line 64
64:     def initialize(seq, antisense_size = 21, max_gc_percent = 60.0, min_gc_percent = 40.0)
65:       @seq = seq.rna!
66:       @pairs = Array.new
67:       @antisense_size = antisense_size
68:       @max_gc_percent = max_gc_percent
69:       @min_gc_percent = min_gc_percent
70:     end

Public Instance methods

design(rule = 'uitei')

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

[Source]

     # File lib/bio/util/sirna.rb, line 105
105:     def design(rule = 'uitei')
106:       @target_size = @antisense_size + 2
107: 
108:       target_start = 0
109:       @seq.window_search(@target_size) do |target|
110:         antisense = target.subseq(1, @target_size - 2).complement.rna
111:         sense     = target.subseq(3, @target_size)
112: 
113:         target_start += 1
114:         target_stop  = target_start + @target_size
115: 
116:         antisense_gc_percent = antisense.gc_percent
117:         next if antisense_gc_percent > @max_gc_percent
118:         next if antisense_gc_percent < @min_gc_percent
119:         
120:         case rule
121:         when 'uitei'
122:           next unless uitei?(target)
123:         when 'reynolds'
124:           next unless reynolds?(target)
125:         else
126:           raise NotImplementedError
127:         end
128: 
129:         pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
130:         @pairs.push(pair)
131:       end
132:       return @pairs
133:     end
reynolds()

same as design(‘reynolds’).

[Source]

     # File lib/bio/util/sirna.rb, line 100
100:     def reynolds
101:       design('reynolds')
102:     end
reynolds?(target)

Reynolds’ rule.

[Source]

    # File lib/bio/util/sirna.rb, line 88
88:     def reynolds?(target)
89:       return false if /[GC]{9}/i =~ target
90:       return false unless /^.{4}A.{6}U.{2}[AUC].{5}[AU].{2}$/i =~ target
91:       return true
92:     end
uitei()

same as design(‘uitei’).

[Source]

    # File lib/bio/util/sirna.rb, line 95
95:     def uitei
96:       design('uitei')
97:     end
uitei?(target)

Ui-Tei‘s rule.

[Source]

    # File lib/bio/util/sirna.rb, line 73
73:     def uitei?(target)
74:       return false unless /^.{2}[GC]/i =~ target
75:       return false unless /[AU].{2}$/i =~ target
76:       return false if     /[GC]{9}/i   =~ target
77: 
78:       one_third  = target.size * 1 / 3
79:       start_pos  = @target_size - one_third - 1
80:       remain_seq = target.subseq(start_pos, @target_size - 2)
81:       au_number  = remain_seq.scan(/[AU]/i).size
82:       return false if au_number < 5
83:   
84:       return true
85:     end

[Validate]