Biological information signal processor

Abstract

The computation requirements for mapping and sequencing the human genome might soon exceed the capability of any existing supercomputer. The systolic array processor presented in this paper, called biological information signal processor (BISP), has the capability to satisfy the current and anticipated future computational requirements for performing sequence comparisons based on the T.F. Smith and M.S. Waterman algorithm (1981) as extended by M.S. Waterman and M. Eggert (1987). The BISP can conduct the most time consuming sequence comparison functions, establishing both global and local relationships between two sequences. A modified Smith and Waterman algorithm is presented in this paper for efficient VLSI implementation. Methods are developed to reduce the BISP systolic array I/O bandwidth problem by reporting only the statistical significant results. Estimated performance of the BISP is compared with several different computer architectures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>