A Speculative HMMER Search Implementation on GPU

Due to the exponentially growing bioinformatics databases and rapidly popular of GPU for general purpose computing, it is promising to employ GPU techniques to accelerate the sequence search process. Hmmsearch from HMMER bioinformatics software package is a wildly used software tool for sensitive profile HMM (Hidden Markov Model) searches of biological sequence databases. In this paper, we implement a speculative hmmsearch implementation on NVIDIA Fermi GPU and apply various optimizations to it. We test the enhancements in our GPU implementation in order to demonstrate the effectiveness of optimization strategies. Result shows that our speculative hmmsearch implementation achieves up to 6.5x speedup over previous fast single-threaded SSE implementation.