• DocumentCode
    2724450
  • Title

    Towards Fast Bioinformatics Algorithms: Benchmarking the GPGPU

  • Author

    Alic, Andrei ; Visan, Simona ; Potolea, Rodica

  • Author_Institution
    Tech. Univ. of Cluj-Napoca, Cluj-Napoca, Romania
  • fYear
    2011
  • fDate
    6-8 July 2011
  • Firstpage
    258
  • Lastpage
    261
  • Abstract
    This paper studies the viability of GPGPU, by analyzing the speedup of 9 algorithms frequently used in practice. The speedup we have obtained suggests the possibility of implementing fast versions of Levenshtein distance and Knuth-Morris-Pratt exact search, required by many bioinformatics applications.
  • Keywords
    bioinformatics; computer graphic equipment; coprocessors; GPGPU; Knuth-Morris-Pratt exact search; Levenshtein distance; fast bioinformatics algorithm; general purpose graphics processing unit; Arrays; Bioinformatics; Clustering algorithms; Graphics processing unit; Instruction sets; Partitioning algorithms; Random access memory; GPGPU; bioinformatics; implementation; parallel algorithms;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Parallel and Distributed Computing (ISPDC), 2011 10th International Symposium on
  • Conference_Location
    Cluj Napoca
  • Print_ISBN
    978-1-4577-1536-5
  • Type

    conf

  • DOI
    10.1109/ISPDC.2011.45
  • Filename
    6108282
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=2724450