Combining execution pipelines to improve parallel implementation of HMMER on FPGA

HMMER is a widely used tool in bioinformatic, based on the Profile Hidden Markov Models. The computation kernels of HMMER, namely MSV and P7Viterbi are very compute intensive, and their data dependencies if interpreted naively, lead to a purely sequential execution. In this paper, we propose a original parallelization scheme for HMMER by rewriting the mathematical formulation, to expose hidden potential parallelization opportunities. Our parallelization scheme targets FPGA technology, and our architecture can achieve 10 times speedup compared with the latest HMMER3 SSE version, without compromising on the sensitivity of original algorithm.