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Is There An Implementation Of Dnabit Compress Algorithm?

I'm looking at:

And the sample implementation of the algorithm seems to be broken (I see missing closing brackets for starters).

Does anyone has a working implementation? Thank you!

dna
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updated by Biostar Biostar • written by Martyix • Martyix

Have you tried contacting the authors?

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written by Sean Davis Sean Davis

Well, it seems to be the only possibility left. So I'll try that.

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written by Martyix • Martyix

well - frankly - when the sample implementation does not work I usually move on

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written by Istvan Albert Istvan Albert

1 answer

That algorithm is nonsense. First off, they claim to compress arbitrary DNA into no more than 1.58 bits per base, which is of course impossible. And if you read their paper, you'll find that different DNA sequences give rise to the same code. You're much better off just using gzip.

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written by Marvin • Marvin

you need two bits to represent a,c,g,t. however, runs of the same 2-bit representation of the same nucleotide can be further compressed with block compression or BW.

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written by Aaronquinlan Aaronquinlan

Right, but they're claiming 1.58 bits in the "worst-case" scenario, which is rubbish. Perhaps that was its performance on the worst one they happened to test, but there have to be input cases that have a minimum of 2 bits per base.

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written by Fwip Fwip

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