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In this paper, we study methods for improving the efficiency and privacy ofcompressed DNA sequence comparison computations, under various queryingscenarios. For instance, one scenario involves a querier, Bob, who wants totest if his DNA string, $Q$, is close to a DNA string, $Y$, owned by a dataowner, Alice, but Bob does not want to reveal $Q$ to Alice and Alice is willingto reveal $Y$ to Bob \emph{only if} it is close to $Q$. We describe aprivacy-enhanced method for comparing two compressed DNA sequences, which canbe used to achieve the goals of such a scenario. Our method involves areduction to set differencing, and we describe a privacy-enhanced protocol forset differencing that achieves absolute privacy for Bob (in the informationtheoretic sense), and a quantifiable degree of privacy protection for Alice.One of the important features of our protocols, which makes them ideally suitedto privacy-enhanced DNA sequence comparison problems, is that the communicationcomplexity of our solutions is proportional to a threshold that bounds thecardinality of the set differences that are of interest, rather than thecardinality of the sets involved (which correlates to the length of the DNAsequences). Moreover, in our protocols, the querier, Bob, can easily computethe set difference only if its cardinality is close to or below a specifiedthreshold.

Privacy-Enhanced Methods for Comparing Compressed DNA Sequences