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Performing DNA comparison on a bio-inspired tissue of FPGAs | IEEE Conference Publication | IEEE Xplore

Performing DNA comparison on a bio-inspired tissue of FPGAs


Abstract:

String comparison is a critical issue in many application domains, including speech recognition, contents search, and bioinformatics. The similarity between two strings o...Show More

Abstract:

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 /spl times/ 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 Needleman-Wunsh 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 Needleman-Wunsh 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 architecture.
Date of Conference: 22-26 April 2003
Date Added to IEEE Xplore: 28 July 2003
Print ISBN:0-7695-1926-1
Print ISSN: 1530-2075
Conference Location: Nice, France

References

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