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Title: A protein sequence analysis hardware accelerator based on divergences
Authors: Eusse, Juan Fernando
Moreano, Nahri
Melo, Alba Cristina Magalhães Alves de
Jacobi, Ricardo Pezzuol
Assunto:: Algoritmos genéticos
Programação genética (Computação)
Sequência de bases
Issue Date: 2012
Publisher: Hindawi Publishing Corporation
Citation: EUSSE, Juan Fernando et al. A protein sequence analysis hardware accelerator based on divergences. International Journal of Reconfigurable Computing, New York, v. 2012, Article ID 201378, 19 p., 2012. Disponível em: <http://www.hindawi.com/journals/ijrc/2012/201378/>. Acesso em: 28 fev. 2013. doi:10.1155/2012/201378
Abstract: 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.
Licença:: 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. Fonte: http://www.hindawi.com/journals/ijrc/2012/201378/. Acesso em: 28 fev. 2013.
DOI: doi:https://dx.doi.org/10.1155/2012/201378
Appears in Collections:CIC - Artigos publicados em periódicos

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