BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.

ABSTRACT: Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the sa

SUBMITTER: Firtina C 

PROVIDER: S-EPMC9853099 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature