Multiple sequence alignment on an FPGA

Molecular Biologists frequently compute multiple sequence alignments (MSAs) to identify similar regions in protein families. Progressive alignment is a widely used approach to compute MSAs. However, aligning a few hundred sequences by popular progressive alignment tools requires several hours on sequential computers. Due to the rapid growth of biological sequence databases biologists have to compute MSAs in afar shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. To derive an efficient mapping onto this type of architecture, fine-grained parallel processing elements (PEs) have been designed. Using this PE design as a building block we have constructed a linear systolic array to perform a pairwise sequence distance computation using dynamic programming. This results in an implementation with significant runtime savings on a standard off-the-shelf FPGA.