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Volume 2 / Issue 2

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DOI:   10.3217/jucs-002-02-0077


Dedicated Hardware for Biological Sequence Comparison

Dominique Lavenier (IRISA, Campus de Beaulieu, France)

Abstract: Biological sequence comparison is a time consuming task on a Von Neuman computer. The addition of dedicated hardware for parallelizing the comparison algorithms results in a reduction of several orders of magnitude in the execution time. This paper presents and compares different dedicated approaches, based on the parallelization of the algorithms on linear arrays of processors.

Keywords: Biological Sequence Comparison, DNA, FPGA, Hardware, VLSI

Categories: B.7.1