Approximate k-Mer matching usingfuzzy hash maps

John Healy; Desmond Chambers

doi:10.1109/TCBB.2014.2309609

Approximate k-Mer matching usingfuzzy hash maps

John Healy, Desmond Chambers

Galway-Mayo Institute of Technology

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

7 Citations (Scopus)

Abstract

We present a fuzzy technique for approximate $k$-mer matching that combines the speed of hashing with the sensitivity of dynamic programming. Our approach exploits the collision detection mechanism used by hash maps, unifying the two phases of 'seed and extend' into a single operation that executes in close to $O$(1) average time.

Original language	English
Article number	6758383
Pages (from-to)	258-264
Number of pages	7
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume	11
Issue number	1
DOIs	https://doi.org/10.1109/TCBB.2014.2309609
Publication status	Published - 2014

Keywords

Biology and genetics
fuzzy set

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10.1109/TCBB.2014.2309609

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Approximate k-Mer matching usingfuzzy hash maps

Abstract

Keywords

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