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An FPGA-Based Web Server for High Performance Biological Sequence Alignment

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.