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.
|Number of pages||8|
|Publication status||Published - 2009|
|Event||Adaptive Hardware and Systems, 2009. AHS 2009. NASA/ESA Conference on - San Francisco, Canada|
Duration: 29 Jul 2009 → 1 Aug 2009
|Conference||Adaptive Hardware and Systems, 2009. AHS 2009. NASA/ESA Conference on|
|Period||29/07/09 → 1/08/09|