• DocumentCode
    22373
  • Title

    Approximate k -Mer Matching Using Fuzzy Hash Maps

  • Author

    Healy, John ; Chambers, David H.

  • Author_Institution
    Dept. of Comput. & Math., Galway-Mayo Inst. of Technol., Galway, Ireland
  • Volume
    11
  • Issue
    1
  • fYear
    2014
  • fDate
    Jan.-Feb. 2014
  • Firstpage
    258
  • Lastpage
    264
  • 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.
  • Keywords
    bioinformatics; dynamic programming; fuzzy set theory; approximate k-Mer matching; collision detection; dynamic programming; fuzzy hash maps; fuzzy technique; single operation; Bioinformatics; Computational biology; Genomics; Heuristic algorithms; Indexes; Prototypes; Sensitivity; Biology and genetics; fuzzy set;
  • fLanguage
    English
  • Journal_Title
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on
  • Publisher
    ieee
  • ISSN
    1545-5963
  • Type

    jour

  • DOI
    10.1109/TCBB.2014.2309609
  • Filename
    6758383
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=22373