3 ms·
Degenerate nucleotide matching (using this method) is only possible with 4 bits of data. If BLAT is using this method for counting matches, I'm unaware. The al
by keithwhor 12y ago
Degenerate nucleotide matching (using this method) is only possible with 4 bits of data.
If BLAT is using this method for counting matches, I'm unaware. The algorithm is reliant on storing nucleotides in 4 bits, so I doubt it uses this exact method.
- dekhn 12y agoActually, given huffman coding, you can do it with fewer than 4 because the degenerates are so rare.
- keithwhor 12y agoKills the algorithm (as described here) performance when you have nonstandard nucleotide widths (in bits). Rather, makes it completely unsuitable. It's dependent upon fixed-width binary data.