Two Efficient Techniques to Find Approximate Overlaps between Sequences

Algorithm 3

Solving AAPSP using pigeonhole principle.

 for Every read in input reads do

  for Every candidate suffix in do

   for Every part of length in ’s prefix do

     if p is found in position in the index then

       for Every read found in do

        compare all characters before with

            their corresponding characters in

         if threshold is not reached then

           compare all characters after with

               their corresponding characters in

               until the end of is reached

         end if

         if threshold is not reached then

           report as a suffix prefix match between and

         end if

       end for

     end if

   end for

  end for

 end for