论文信息 - Hardware-based Comparison Of DNA Sequences

Hardware-based Comparison Of DNA Sequences

DNA sequence comparison is becomin an increasingly important activity as the volume of DNfA that has been sequenced increases. The most widely used algorithms for the comparison of two sequences of DNA are O(m.n) on the lengths, m and n, of the sequences being compared, though significant speedu s are available both through improved algorithms and parisle1 hardware implementations. This paper describes a s stem based on commercial1 available integrated circyits whicZ cpmpares DNA sequences Q correlation in time that is O(n). Usmg a hardware-based correlator connected to the expansion bus of an IBM PC compatible com uter we were able to achieve a speed up of 4 orders of magnitule over a softwarebased implementation of the correlation techruque.

E. A. Cheever | M. L. Wennemyr | W. A. Karunaratne | David B. Searls

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