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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.

user3335040
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  • If you want to find all possible alignments, something along the lines of Needleman-Wunch or Smith-Waterman is the only option - you need to try all possible alignments, and dynamic programming (which is the crux of both of those algorithms) is pretty much the only way to try them all efficiently. Any other algorithm, such as BLAST, will be a heuristic approach, which may be faster but will lose the guarantees that it sounds like you want. – seaotternerd Apr 20 '15 at 02:49

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you can use BLAST for Basic Local Alignment Search Tool

official site or wiki

Amson
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