Hardware-Based Comparison Of DNA Sequences
Proceedings Of The Annual International Conference Of The IEEE Engineering In Medicine And Biology Society
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.
J. H. Nagel and W. M. Smith
Annual International Conference Of The IEEE Engineering In Medicine And Biology Society, 1991
October 31-November 3, 1991
Erik Allen Cheever , '82; Magnus L. Wennemyr , '89; William A. Karunaratne , '91; and D. B. Searls.
"Hardware-Based Comparison Of DNA Sequences".
Proceedings Of The Annual International Conference Of The IEEE Engineering In Medicine And Biology Society.