Where can I find a good SSE-vectorized Smith-Waterman implementation in C?

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Claudia Misale

Here is

http://calvados.di.unipi.it/dokuwiki/doku.php?id=ffnamespace:about

You can find, among examples, a SSE-vectorized implementation of Smith-Waterman algorithm implemented on top of FastFlow parallel programming framework. In this second link you can find the related paper (“Efficient Smith-Waterman on multi-core with FastFlow). Hope it is useful.

http://alpha.di.unito.it/parallel-programming-papers/

Dag Lyberg

Thanks Claudia. I could run a test to compare FF to other implementations, but I do not know yet.

I am going to do many SW alignments on pairs of DNA sequences. Most of these sequences are no longer than 30 nt (1 nucleotide/nt = 1 character). My current idea is to run an SSE-vectorized implementation on each pairwise SW alignment, and have an parallel algorithm that runs one such alignment at a time per core.

I think that your paper has the idea of running several cores per SW alignment for long DNA sequences. That is different to what I am looking for.