Approximate k-Mer matching usingfuzzy hash maps

John Healy, Desmond Chambers

Research output: Contribution to journalArticlepeer-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 languageEnglish
Article number6758383
Pages (from-to)258-264
Number of pages7
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume11
Issue number1
DOIs
Publication statusPublished - 2014

Keywords

  • Biology and genetics
  • fuzzy set

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