Parallel Sequence Alignment Algorithm

Question

I am working on implementing an efficient sequence alignment algorithm using parallelism in Java. I want to return all the possible positions of the sequence.

Can you guys suggest an algorithm for which this is doable? I have looked into the Needem-Wunsch an Smith-Waterman but I am looking for something a little less complex but that still is efficient. I have just started working with parallelism so it cannot be too complex.

Thanks.

Answer 1

you can use BLAST for Basic Local Alignment Search Tool

official site or wiki