There are proprietary libraries (in C) that do this sort of thing in a couple milliseconds per query string. The basic idea is that you use your dictionary of sequences to construct a finite automaton, which either accepts or rejects your query string. This does require some cleverness to do fuzzy matching, and I'm afraid I don't know enough of the details to help you out there.

In reply to Re^2: Fuzzy Searching: Optimizing Algorithm Selection by kscaldef
in thread Fuzzy Searching: Optimizing Algorithm Selection by Itatsumaki

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