[keithwhor]

While regex could replace the conditional check in the "initial" (string-only) implementation to allow for degenerate nucleotide matching, it would certainly not speed it up there.

Additionally, I'm not sure how you'd intend to do the exhaustive alignment checks / scoring with a regex. (I want to find all sequences that match my 20-mer with an identity score of at least 14/20 --- what's my well-formed regex for that? There are 38,760 different ways to choose 14 of 20 nucleotides.)

Plus, there's the added overhead of having to come up with a well-formed regex to begin with. :)