A perceptual hash function to store and retrieve large scale DNA sequences

TL;DR

This paper introduces a novel perceptual hash function based on DCT-SO for efficient storage and retrieval of large-scale DNA sequences, enabling similarity comparison without cryptographic hash limitations.

Contribution

The paper adapts perceptual hashing techniques, specifically DCT-SO, for DNA sequences, providing a data-efficient method for similarity-based retrieval of massive genomic data.

Findings

Effective data reduction achieved

Hash comparison via Hamming Distance is viable

Method successfully retrieves similar DNA sequences

Abstract

This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences. Perceptual hash function presented here is based on a Discrete Cosine Transform Sign Only (DCT-SO). Each nucleotide is encoded as a fixed gray level intensity pixel and the hash is calculated from its significant frequency characteristics. This results to a drastic data reduction between the sequence and the perceptual hash. Unlike cryptographic hash functions, perceptual hashes are not affected by "avalanche effect" and thus can be compared. The similarity distance between two hashes is estimated with the Hamming Distance, which is used to retrieve DNA sequences. Experiments that we conducted show that our approach is relevant for storing massive DNA sequences, and retrieving them.