An FPGA-based accelerator for multiple biological sequence alignment with DIALIGN

Authors:
Azzedine Boukerche;Jan Mendonca Correa;Alba Cristina Magalhaes Alves de Melo;Ricardo Pezzuol Jacobi;Adson Ferreira Rocha
Affiliations:
SITE-School of Information Technology and Engineering, University of Ottawa, Canada;Department of Computer Science, University of Brasilia, Brazil;Department of Computer Science, University of Brasilia, Brazil;Department of Computer Science, University of Brasilia, Brazil;Department of Electrical Engineering, University of Brasilia, Brazil
Venue:
HiPC'07 Proceedings of the 14th international conference on High performance computing
Year:
2007

Citing 5
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The multiple sequence alignment problem in biology

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Algorithms on strings, trees, and sequences: computer science and computational biology
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To Accelerate Multiple Sequence Alignment using FPGAs

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Parallel strategies for the local biological sequence alignment in a cluster of workstations

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Abstract

Multiple sequence alignment (MSA) is a very important problem in Computational Biology since it is often used to identify evolutionary relationships among the organisms and predict secondary/tertiary structure. Since MSA is known to be a computationally challenging problem, many proposals were made to accelerate it either by using parallel processing or hardware accelerators. In this paper, we propose an FPGA based accelerator to execute the most compute intensive part of DIALIGN, an iterative method to obtain multiple sequence alignments. The experimental results collected in our 200- element FPGA prototype show that a speedup of 383.41 was obtained when compared with the software implementation.