Class: Bioroebe::SiRNA

Inherits:
Object
  • Object
show all
Defined in:
lib/bioroebe/siRNA/siRNA.rb

Overview

Bioroebe::SiRNA

Instance Method Summary collapse

Constructor Details

#initialize(i = ARGV) ⇒ SiRNA

#

initialize

#

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# File 'lib/bioroebe/siRNA/siRNA.rb', line 42

def initialize(i = ARGV)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  @sequence = i
end

Instance Method Details

#reynolds?(i = @sequence, be_verbose = true) ⇒ Boolean Also known as: reynolds_rule?

#

reynolds?

This method implements the reynolds' rule.

The Reynolds' rule does not require to fulfill all the criteria simultaneously.

See: www.nature.com/articles/nbt936

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/siRNA/siRNA.rb', line 108

def reynolds?(
    i          = @sequence,
    be_verbose = true
  )
  unless i.size == 23 # 21 nt target + 2 nt overhang
    if be_verbose
      puts 'The size should be 23; it is '+i.to_s.size.to_s+'.'
    end
    return false
  end
  score = 0
  seq19 = i[2 .. 20] # 19 nt double-stranded region of siRNA
  complement_to_seq19 = ::Bioroebe.reverse_complement(seq19) # This is actually the reverse complement.
  # ======================================================================= #
  # === criterium 1
  # ======================================================================= #
  gc_number = seq19.scan(/[GC]/i).size
  if (7 <= gc_number and gc_number <= 10)
    score += 1
  end
  # ======================================================================= #
  # === criterium 2
  # ======================================================================= #
  au_number = seq19[14..18].scan(/[AU]/i).size
  score += au_number
  # ======================================================================= #
  # === criterium 3
  #
  # This is not yet implemented: Tm
  # ======================================================================= #
  # ======================================================================= #
  # === criterium 4
  # ======================================================================= #
  score += 1 if seq19[18..18].match(/A/i)
  # ======================================================================= #
  # === criterium 5
  # ======================================================================= #
  score += 1 if seq19[2..2].match(/A/i)
  # ======================================================================= #
  # === criterium 6
  # ======================================================================= #
  score += 1 if seq19[9..9].match(/[U]/i)
  # ======================================================================= #
  # === criterium 7
  # ======================================================================= #
  score -= 1 if seq19[18..18].match(/[GC]/i)
  # ======================================================================= #
  # === criterium V8
  # ======================================================================= #
  score -= 1 if seq19[12..12].match(/G/i)
  if score >= 6
    return score
  else
    return false
  end
end

#uitei?(i = @sequence, be_verbose = true) ⇒ Boolean Also known as: uitei_rule?

#

uitei?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/siRNA/siRNA.rb', line 52

def uitei?(
    i          = @sequence,
    be_verbose = true
  )
  unless i.size == 23 # 21 nt target + 2 nt overhang
    if be_verbose
      puts 'The size should be 23; it is '+i.to_s.size.to_s+'.'
    end
    return false
  end
  seq19 = i[2 .. 20] # 19 nt double-stranded region of siRNA
  complement_to_seq19 = ::Bioroebe.reverse_complement(seq19) # This is actually the reverse complement.
  # ======================================================================= #
  # === criterium 1
  #
  # (1) A/U at the 5' end of the antisense strand. This can be checked
  #     if we take the last nucleotide from the sense strand. Note
  #     that ineffective siRNAs are G or C here.
  # ======================================================================= #
  last_nucleotide = complement_to_seq19[0, 1]
  return false unless last_nucleotide.match(/T|A|U/i) # Match either T or A.
  # ======================================================================= #
  # === criterium 2
  #
  # (2) G/C at the 5' end of the sense strand
  # ======================================================================= #
  return false unless seq19.start_with?(/G|C/i)
  # ======================================================================= #
  # === criterium 3
  #
  # (3) at least five A/U residues in the 5' terminal one-third
  #     of the antisense strand (this means leading area, but
  #     on the antisense strand, so T and A there)
  # ======================================================================= #
  one_third = (seq19.size / 3)+1
  number_of_AU_residues = complement_to_seq19[0, one_third].scan(/A|T|U/i).size
  return false unless number_of_AU_residues > 4
  # ======================================================================= #
  # === criterium 4
  #
  # (4) the absence of any GC stretch of more than 9 nt in length
  # ======================================================================= #
  return false if seq19.match(/G{10}|C{10}/i)
  return true # This is then the new default return value here.
end