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© Oxford University Press

A special-purpose processor for gene sequence analysis

Barry Fagin , J.Gill Watt 1 and Robert Gross 2

Thayer School of Engineering, Dartmouth College Hanover, NH 03755, USA
1Department of Biology, Dartmouth College Hanover, NH 03755, USA

Advances in computational biology have occurred primarily in the areas of software and algorithm development; new designs of hardware to support biological computing are extremely scarce. This is due, we believe, to the presence of a non-trivial knowledge gap between molecular biologists and computer designers. The existence of this gap is unfortunate, as it has long been known that for certain problems, special-purpose computers can achieve significant cost/performance gains over general-purpose machines. We describe one such computer here: a custom accelerator for gene sequence analysis. The accelerator implements a version of the Needleman – Wunsch algorithm for nucleotide sequence alignment. Sequence lengths are constrained only by available memory; the product of sequence lengths in the current implementation can be up to 222. The machine is implemented as two NuBus boards connected to a Mac IIf/x, using a mixture of TTL and FPGA technology clocked at 10 MHz. The boards are completely functional, and yield a 15-fold performance improvement over an unassisted host.

Received on May 11, 1992; accepted on July 15, 1992

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