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

Ying Liu, Khaled Benkrid, AbdSamad Benkrid, S. Kasap

Research output: Chapter in Book/Report/Conference proceedingConference proceeding

11 Citations (Scopus)

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
Title of host publicationProceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009
PublisherIEEE
Pages361-368
Number of pages8
ISBN (Print)978-0-7695-3714-6
DOIs
Publication statusPublished - 10 Nov 2009
Externally publishedYes
Event2009 NASA/ESA Conference on Adaptive Hardware and Systems - San Francisco, United States
Duration: 29 Jul 20091 Aug 2009

Conference

Conference2009 NASA/ESA Conference on Adaptive Hardware and Systems
CountryUnited States
CitySan Francisco
Period29/07/091/08/09

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  • Cite this

    Liu, Y., Benkrid, K., Benkrid, A., & Kasap, S. (2009). An FPGA-based web server for high performance biological sequence alignment. In Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009 (pp. 361-368). IEEE. https://doi.org/10.1109/AHS.2009.59