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One of the basic tasks in bioinformatics is localizing a short subsequence$S$, read while sequencing, in a long reference sequence $R$, like the humangeneome. A natural rapid approach would be finding a hash value for $S$ andcompare it with a prepared database of hash values for each of length $|S|$subsequences of $R$. The problem with such approach is that it would only spota perfect match, while in reality there are lots of small changes:substitutions, deletions and insertions.  This issue could be repaired if having a hash function designed to toleratesome small distortion accordingly to an alignment metric (likeNeedleman-Wunch): designed to make that two similar sequences should mostlikely give the same hash value. This paper discusses construction ofDistortion-Resistant Hashing (DRH) to generate such fingerprints for rapidsearch of similar subsequences. The proposed approach is based on the ratedistortion theory: in a nearly uniform subset of length $|S|$ sequences, thehash value represents the closest sequence to $S$. This gives some control ofthe distance of collisions: sequences having the same hash value.

Distortion-Resistant Hashing for rapid search of similar DNA subsequence