An FPGA-based accelerator for multiple biological sequence alignment with DIALIGN

Abstract

Multiple sequence alignment (MSA) is a very important problem in Computational Biology since it is often used to identify evolutionary relationships among the organisms and predict secondary/tertiary structure. Since MSA is known to be a computationally challenging problem, many proposals were made to accelerate it either by using parallel processing or hardware accelerators. In this paper, we propose an FPGA based accelerator to execute the most compute intensive part of DIALIGN, an iterative method to obtain multiple sequence alignments. The experimental results collected in our 200-element FPGA prototype show that a speedup of 383.41 was obtained when compared with the software implementation. © Springer-Verlag Berlin Heidelberg 2007.