Re: [Seqan-dev] Combine bit-parallel algorithm with Ukkonens trick for globalAlignment

["Weese, David" <weese@campus.fu-berlin.de>]

Hi Lingjie,

yes, the implementation of Myers' bitvector algorithm for large patterns incorporates the Ukkonen algorithm to save computation time.

Cheers,

David

Am 16.06.2011 um 01:32 schrieb Lingjie Weng:

Dear Seqan team,

I am interested in our Seqan C++ library, it is really helpful. I am curious whether "MyersBitVector " algorithm in globalalignment has already combined with Ukkonens algorithm.

I found you have MyersUkkonen in pattern matching, I am wondering if you have such implementation which could be used for sequence alignment, mainly for computing the levenshtein edit distance. Thank you for your patience.

Thanks,
Lingjie

PhD student
University of California, Irvine

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