Design of a Hardware Board for Sequence Alignment

T. Kato ([1]
M. Taiji ([2]
T. Ebisuzaki ( [2]
A. Suyama ([1]

[1] Department of Life Sciences,
[2] Department of Earth Science and Astronomy,

Graduate School of Arts and Sciences, The University of Tokyo

3-8-1 Komaba, Meguro-ku, Tokyo 153, Japan


We have designed a special hardware board to calculate optimal alignments of two sequences based on the Myers-Miller dynamic programming algorithm. The board was designed to be able to calculate each similarity or distance matrix element in parallel in one system clock pulse. The present version of the board had four pipelines and thus can calculate 120 million matrix elements per one second.