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Performing DNA Comparison on a Bio-Inspired Tissue of FPGAs

9 years 6 months ago
Performing DNA Comparison on a Bio-Inspired Tissue of FPGAs
String comparison is a critical issue in many application domains, including speech recognition, contents search, and bioinformatics. The similarity between two strings of lengths N and M can be computed in O(N × M) steps by means of a dynamic programming algorithm developed by Needleman and Wunsh. The algorithm can be effectively mapped onto a systolic array, resulting in a parallel implementation that executes in O(N + M) steps. In this paper we present a parallel implementation of the NeedlemanWunsh algorithm on the BioWall, a giant reconfigurable computing tissue conceived to prototype bio-inspired cellular systems. Our implementation is not aimed at competing with existing parallel implementations of the NeedlemanWunsh algorithm, since the BioWall suffers from the typical performance limitations of a large prototyping platform. Rather, it is a significant design experience in the field of reconfigurable computing because of the bio-inspired peculiarities of the BioWall archi...
Matteo Canella, Filippo Miglioli, Alessandro Bogli
Added 04 Jul 2010
Updated 04 Jul 2010
Type Conference
Year 2003
Where IPPS
Authors Matteo Canella, Filippo Miglioli, Alessandro Bogliolo, Enrico Petraglio, Eduardo Sanchez
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