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

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 energyefficient.

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

“…A fairer comparison in speed would take the results of sequence length 256 since it is close to the average sequence length in the SWISS-PROT database (360). Each PE in the FPGA systolic array consumes ∼110 slices, and, consequently, we were able to fit ∼500 PEs on a Xilinx Virtex-4 LX160-11 FPGA [22]. Moreover, the processing word length in the FPGA systolic array is 16 bits, and the circuit was clocked at 80 MHz.…”

Hardware Implementation of Web Based Arabic Optical Character Recognition Units

“…An FPGA-based web server that is targeted for biological alignment has been designed and implemented in [18]. In their approach a host application receives queries from users and submits them to the FPGAs coprocessors.…”

“…Although all previously mentioned implementation approaches are feasible as these approaches or similar ones have been proposed in literature like those presented in [15][16][17][18][19][20][21][22][23][24], we will suggest to go for the approach where the web server is not embedded in the FPGA as this approach is much simpler to implement. However, some tuning and modifications are required in order to have the system function properly.…”

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

“…Others such as [19], [28], [33] provide generic, parameterizable FPGA cores for PSA which are portable across various FPGA platform. Finally, Liu et al [34] introduce the concept of "RC-PSA in the cloud" where a web server is used to serve alignment requests. All these implementations, compared to state-of-the-art CPU designs, can deliver a speedup of more than 62×.…”