Fast Sequence Alignment on Unicode Strings

Question

I want to run something like the BLAST algorithm to query a large database of unicode strings. Most of the alignment software like BLAST expects nucleotide or protein strings as input. But my input could potentially contain any unicode character. Is anyone aware of a piece of software that will let me do this? The scoring matrix could just be the identity matrix (no partial matching.)

I have tried Needleman-Wunsch and Smith Waterman but for my purposes they are too slow. I need to query a large database, as in BLAST.

Thank you!

I'm not sure I understand the purpose; for bioinformatics questions, you might also want to try http://biostar.stackexchange.com/ — PhiS, Aug 04 '10 at 19:08

score 0 · Answer 1 · edited Oct 06 '12 at 09:01

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You might as well give STELLAR a try: It is a quasar-like filter algorithm with verification step. (see this paper)

It is quite fast for low edit distances <5%.

edited Oct 06 '12 at 09:01

matthias krull

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answered Aug 22 '12 at 07:56

Ragnik

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score 0 · Answer 2 · answered Sep 02 '10 at 20:35

BLAST can be used to align sequences of characters from any alphabet. You will probably need to implement it yourself, since most of the publicly available implementations are tailored to proteins, but the algorithm is not specific to proteins or nucleotide sequences.

score 0 · Answer 3 · answered Aug 08 '11 at 15:03

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vmatch is a general suffix-tree based alignment program

answered Aug 08 '11 at 15:03

Jeremy Leipzig

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Fast Sequence Alignment on Unicode Strings

3 Answers3