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

Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by DannyBee on Monday February 23, 2015 @01:08PM (#9095814)

The method you are using for comparison is commonly simdized and used for string matching.

Note also that intel/AMD SSE4+ has a 32 bit/64 bit popcnt instruction with 3 cycle latency/1 cycle throughput (for both 32 bit and 64 bit version), and so is faster for counting bits/matches than any of the methods you are using :)

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by keithwhor on Monday February 23, 2015 @01:37PM (#9096007)

Nice! Would love to see it implemented - though that popcnt instruction isn't accessible via JavaScript as far as I'm aware. ;)

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by DannyBee on Monday February 23, 2015 @01:59PM (#9096179)

Also note - your while loop isn't 0 cycles, in fact, it's probably worse than the bit-twiddling depending on sparseness.

This is because the test and branch always happens, and is essentially guaranteed to be mispredicted a lot.

These branch mispredictions are likely to cost a lot more than the n cycles it theoretically saves.

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