International Journal of Reconfigurable Computing - Special issue on selected papers from the international workshop on reconfigurable communication-centric systems on chips (ReCoSoC' 2010)
The Journal of Supercomputing
A data parallel strategy for aligning multiple biological sequences on multi-core computers
Computers in Biology and Medicine
Self-Alignment Schemes for the Implementation of Addition-Related Floating-Point Operators
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
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The recent and astonishing accomplishments in the field of Genomics would not have been possible without the techniques, algorithms, and tools developed in Bioinformatics. Biological sequence comparison is an important operation in Bioinformatics because it is used to determine how similar two sequences are. As a result of this operation, one or more alignments are produced. DIALIGN is an exact algorithm that uses dynamic programming to obtain optimal biological sequence alignments in quadratic space and time. One effective way to accelerate DIALIGN is to design FPGA-based architectures to execute it. Nevertheless, the complete retrieval of an alignment in hardware requires modifications on the original algorithm because it executes in quadratic space. In this paper, we propose and evaluate two FPGA-based accelerators executing DIALIGN in linear space: one to obtain the optimal DIALIGN score (DIALIGN-Score) and one to retrieve the DIALIGN alignment (DIALIGN-Alignment). Because it appears to be no documented variant of the DIALIGN algorithm that produces alignments in linear space, we here propose a linear space variant of the DIALIGN algorithm and have designed the DIALIGN-Alignment accelerator to implement it. The experimental results show that impressive speedups can be obtained with both accelerators when comparing long biological sequences: the DIALIGN-Score accelerator achieved a speedup of 383.4 and the DIALIGN-Alignment accelerator reached a speedup of 141.38.