[searine]

Except this is totally reinventing the wheel.

If I want to do fast genome alignment, I'll use lastz which is already blazing fast and written in C. If I want to just look for homology, I'll use blast.

There isn't much need for improved alignment algorithms. If it's a big job, most bioinformatics have access to clusters. If it is a small job, who cares about speed.

[iten]

To be fair, to my knowledge, LASTZ, BLAST, or BLAT don't treat IUPAC ambiguous bases (K, Y, R, etc.) in the way the OP was looking for. That's not to blame the tools, since they have a very good reason not to (they build an index on the target first, and treating ambiguous bases properly would increase the size of the index).

That said, I wonder if grep wouldn't be much faster, since this program is only looking for exact matches, which are easily transformed into a regex by replacing the ambiguous nucleotides with something like (A|T|C).