class Bio::SiRNA::ShRNA

Bio::SiRNA::ShRNA

Designing shRNA.

Attributes

bottom_strand[RW]
top_strand[RW]

Public Class Methods

new(pair) click to toggle source

Input is a Bio::SiRNA::Pair object (the target sequence).

# File lib/bio/util/sirna.rb, line 234
def initialize(pair)
  @pair = pair
end

Public Instance Methods

block_it(method = 'piGENE') click to toggle source

same as design('BLOCK-iT'). method can be one of 'piGENE' (default) and 'BLOCK-iT'.

# File lib/bio/util/sirna.rb, line 251
def block_it(method = 'piGENE')
  top = Bio::Sequence::NA.new('CACC') # top_strand_shrna_overhang
  bot = Bio::Sequence::NA.new('AAAA') # bottom_strand_shrna_overhang
  fwd = @pair.sense
  rev = @pair.sense.complement

  case method
  when 'BLOCK-iT'
    # From BLOCK-iT's manual
    loop_fwd = Bio::Sequence::NA.new('CGAA')
    loop_rev = loop_fwd.complement
  when 'piGENE'
    # From piGENE document
    loop_fwd = Bio::Sequence::NA.new('GTGTGCTGTCC')
    loop_rev = loop_fwd.complement
  else
    raise NotImplementedError
  end

  if /^G/i =~ fwd
    @top_strand    = top + fwd + loop_fwd + rev
    @bottom_strand = bot + fwd + loop_rev + rev
  else
    @top_strand    = top + 'G' + fwd + loop_fwd + rev
    @bottom_strand = bot + fwd + loop_rev + rev + 'C'
  end
end
design(method = 'BLOCK-iT') click to toggle source

only the 'BLOCK-iT' rule is implemented for now.

# File lib/bio/util/sirna.rb, line 239
def design(method = 'BLOCK-iT')
  case method
  when 'BLOCK-iT'
    block_it
  else
    raise NotImplementedError
  end
end
report() click to toggle source

human readable report

# File lib/bio/util/sirna.rb, line 280
def report
  report = "### shRNA\n"
  report << "Top strand shRNA (#{@top_strand.length} nt):\n"
  report << "  5'-#{@top_strand.upcase}-3'\n"
  report << "Bottom strand shRNA (#{@bottom_strand.length} nt):\n"
  report << "      3'-#{@bottom_strand.reverse.upcase}-5'\n"
end