An FPGA-based Web server for high performance biological sequence alignment

Ying Liu, K. Benkrid, Abdsamad Benkrid, S. Kasap

    Research output: Contribution to conferencePaperpeer-review

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    Abstract

    This paper presents the design and implementation of the FPGA-based Web server for biological sequence alignment. Central to this Web-server is a set of highly parameterisable, scalable, and platform-independent FPGA cores for biological sequence alignment. The Web server consists of an HTML-based interface, a MySQL database which holds user queries and results, a set of biological databases, a library of FPGA configurations, a host application servicing user requests, and an FPGA coprocessor for the acceleration of the sequence alignment operation. The paper presents a real implementation of this server on an HP ProLiant DL145 server with a Celoxica RCHTX FPGA board. Compared to an optimized pure software implementation, our FPGA-based Web server achieved a two order of magnitude speed-up for a pairwise protein sequence alignment application based on the Smith-Waterman algorithm. The FPGA-based implementation has the added advantage of being over 100x more energy efficient.
    Original languageEnglish
    Pages361-368
    Number of pages8
    Publication statusPublished - 2009
    EventAdaptive Hardware and Systems, 2009. AHS 2009. NASA/ESA Conference on - San Francisco, Canada
    Duration: 29 Jul 20091 Aug 2009

    Conference

    ConferenceAdaptive Hardware and Systems, 2009. AHS 2009. NASA/ESA Conference on
    CountryCanada
    CitySan Francisco
    Period29/07/091/08/09

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