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There are several problem with that.

  1. Unless you were comparing each sequence against many others, the cost of encoding the sequences is going to exact a high price.
  2. Packing 4 chars per byte is a nice way of doing 1/4 of the work at the xor stage, if you can amortise the conversion. But DNA sequences often contain other characters, N and X for example, and I'm sure I've seen others. I'm not sure what they mean, but I've seen them.

    Once you are down to packing two, 3-bit or 4-bit values per byte, the cost of the encoding gets harder to claw back.

  3. And when you've done the xor, you have to count the results. With the string version, where the null byte means the characters were the same, and anything else, different, the "count the stars" mode of tr/// is an efficient way of achieving this.

    With the bit-encode sequences, you would have to count the zero and non-zero-ness of pairs, or triples or quads of bits. For 2 and 4 bits, this could be done using vec, but not very efficiently. Doing it for triples would be very laborious.


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In reply to Re^3: Hamming Distance Between 2 Strings - Fast(est) Way? by BrowserUk
in thread Hamming Distance Between 2 Strings - Fast(est) Way? by monkfan

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