Hardware Acceleration of HMMER on FPGAs

• Published in: Journal of signal processing systems Vol. 58; no. 1; pp. 53 - 67
• Main Authors: Derrien, Steven, Quinton, Patrice
• Format: Journal Article
• Language: English
• Published: Boston Springer US 2010; Springer
• Subjects: Circuits and Systems; Computer Imaging; Computer Science; Electrical Engineering; Engineering; Hardware Architecture; Image Processing and Computer Vision; Pattern Recognition; Pattern Recognition and Graphics; Signal,Image and Speech Processing; Vision; Reconfigurable computing; HMM; Bioinformatics
• ISSN: 1939-8018; 1939-8115
• DOI: 10.1007/s11265-008-0262-y

We propose a new parallelization scheme for the hmmsearch function of the HMMER software, in order to target FPGA technology. hmmsearch is a very compute intensive software for biological sequence alignment, based on profile hidden Markov models. We derive a flexible, generic, scalable hardware parallel architecture which can accelerate the core of hmmsearch by nearly two orders of magnitude, without modifying the original algorithm of this software. Our derivation is based on the expression of the algorithm as a set of recurrence equations, and we show in a systematic way how a very efficient parallel version of the algorithm can be found by combining scheduling, projection, partitioning, pipelining and precision analysis. We present the performance of the implementation of this parallel algorithm on a FPGA platform.