Title

Hardware-Based Comparison Of DNA Sequences

Document Type

Conference Proceeding

Publication Date

1991

Published In

Proceedings Of The Annual International Conference Of The IEEE Engineering In Medicine And Biology Society

Abstract

DNA sequence comparison is becoming an increasingly important activity as the volume of DNA 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 speedups are available both through improved algorithms and parallel hardware implementations. This paper describes a system based on commercially available integrated circuits which compares DNA sequences by correlation in time that is O(n). Using a hardware-based correlator connected to the expansion bus of an IBM PC compatible computer we were able to achieve a speed up of 4 orders of magnitude over a software-based implementation of the correlation technique.

Published By

IEEE

Editor(s)

J. H. Nagel and W. M. Smith

Conference

Annual International Conference Of The IEEE Engineering In Medicine And Biology Society, 1991

Conference Dates

October 31-November 3, 1991

Conference Location

Orlando, FL

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