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).
Comments
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).