To accelerate multiple sequence alignment using FPGAs

Multiple sequence alignment is a fundamental and challenging problem in computational molecular biology. ClustalW, the most widely used multiple sequence alignment software, performs very slowly on hundreds of sequence. Here, we analyze the algorithm complexity of ClustalW as well as the time profile in practice, and then propose a strategy which uses the reconfigurable hardware FPGA to accelerate ClustalW. Comparison with other coarse-grained parallel strategies demonstrates a fine speedup of this strategy and savage of computing resource