def remove_isolated_residues(seq, len = 2)
      gap_starts = seq.to_enum(:scan, /(-\w{1,#{len}}-)/i).map { |_m| $`.size + 1 }
      # remove isolated residues
      gap_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '-' if isalpha(seq[j]) }
      end
      # remove isolated gaps
      res_starts = seq.to_enum(:scan, /([?\w]-{1,2}[?\w])/i).map { |_m| $`.size + 1 }
      res_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '?' if seq[j] == '-' }
      end
      seq
    end
def remove_isolated_residues(seq, len = 2)
      gap_starts = seq.to_enum(:scan, /(-\w{1,#{len}}-)/i).map { |_m| $`.size + 1 }
      # remove isolated residues
      gap_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '-' if isalpha(seq[j]) }
      end
      # remove isolated gaps
      res_starts = seq.to_enum(:scan, /([?\w]-{1,2}[?\w])/i).map { |_m| $`.size + 1 }
      res_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '?' if seq[j] == '-' }
      end
      seq
    end
Remove isolated residues inside long gaps
 from a given sequence
 Params:
 +seq+:+String+: sequence of residues
 +len+:+Fixnum+: number of isolated residues to be removed
 Output:
 +String+: the new sequence