• DocumentCode
    3703428
  • Title

    Cache and energy efficient alignment of very long sequences

  • Author

    Chunchun Zhao;Sartaj Sahni

  • Author_Institution
    Department of Computer and Information Science and Engineering, University of Florida, United States
  • fYear
    2015
  • Firstpage
    1
  • Lastpage
    6
  • Abstract
    We develop cache and energy efficient algorithms to align very long sequences. These algorithms were evaluated experimentally on a single node of the IBM Blue Gene/Q. We were able to reduce the run time of the classical Myers and Miller linear space alignment algorithm by up to 43%; energy consumption was reduced by up to 45% on our test data.
  • Keywords
    "Heuristic algorithms","Computational modeling","Algorithm design and analysis","Strips","Computers","Prefetching","Approximation algorithms"
  • Publisher
    ieee
  • Conference_Titel
    Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on
  • Type

    conf

  • DOI
    10.1109/ICCABS.2015.7344703
  • Filename
    7344703
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=3703428