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International Journal of Reconfigurable Computing
Volume 2012 (2012), Article ID 201378, 19 pages
Research Article

A Protein Sequence Analysis Hardware Accelerator Based on Divergences

1Electrical Engineering Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
2School of Computing, Federal University of Mato Grosso do Sul, Campo Grande, MS 79070-900, Brazil
3Computer Science Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
4UnB Gama School, University of Brasilia, Gama, DF 72405-610, Brazil

Received 27 September 2011; Accepted 26 December 2011

Academic Editor: Khaled Benkrid

Copyright © 2012 Juan Fernando Eusse et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The Viterbi algorithm is one of the most used dynamic programming algorithms for protein comparison and identification, based on hidden markov Models (HMMs). Most of the works in the literature focus on the implementation of hardware accelerators that act as a prefilter stage in the comparison process. This stage discards poorly aligned sequences with a low similarity score and forwards sequences with good similarity scores to software, where they are reprocessed to generate the sequence alignment. In order to reduce the software reprocessing time, this work proposes a hardware accelerator for the Viterbi algorithm which includes the concept of divergence, in which the region of interest of the dynamic programming matrices is delimited. We obtained gains of up to 182x when compared to unaccelerated software. The performance measurement methodology adopted in this work takes into account not only the acceleration achieved by the hardware but also the reprocessing software stage required to generate the alignment.