Biological information signal processor

Author

Chow, E. ; Hunkapiller, T. ; Peterson, J. ; Waterman, M.S.

Author_Institution

California Inst. of Technol., Pasadena, CA, USA

fYear

1991

fDate

2-4 Sep 1991

Firstpage

144

Lastpage

160

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

Keywords

VLSI; digital signal processing chips; systolic arrays; VLSI implementation; biological information signal processor; computer architectures; human genome; mapping; sequence comparison functions; sequencing; systolic array I/O bandwidth problem; systolic array processor; Bandwidth; Bioinformatics; Biology computing; Genomics; Humans; Signal processing; Signal processing algorithms; Supercomputers; Systolic arrays; Very large scale integration;

fLanguage

English

Publisher

ieee

Conference_Titel

Application Specific Array Processors, 1991. Proceedings of the International Conference on

Conference_Location

Barcelona

Print_ISBN

0-8186-9237-5

Type

conf

DOI

10.1109/ASAP.1991.238887

Filename

238887