How I Wrote an Ultra-Fast DNA Sequence Alignment Algorithm in JavaScript

Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by keithwhor on Monday February 23, 2015 @01:31PM (#9095960)

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.

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by dekhn on Monday February 23, 2015 @04:01PM (#9097013)

Actually, given huffman coding, you can do it with fewer than 4 because the degenerates are so rare.

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by keithwhor on Monday February 23, 2015 @04:20PM (#9097133)

Kills 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.

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