BioSCAN: a VLSI-based system for biosequence analysis

Author

White, C.T. ; Singh, Raj K. ; Reintjes, Peter B. ; Lampe, Jordan ; Erickson, Bruce W. ; Dettloff, Wayne D. ; Chi, Vernon L. ; Altschul, Stephen F.

Author_Institution

North Carolina Univ., Chapel Hill, NC, USA

fYear

1991

fDate

14-16 Oct 1991

Firstpage

504

Lastpage

509

Abstract

A special-purpose computer system has been designed to accelerate scanning large databases of DNA and protein sequences (biosequences) for patterns of interest. The system consists of a custom-designed circuit board installed in a host workstation and associated software. The board features a variable number of identical full-custom ASICs. Each biological sequence comparative analysis node. (BioSCAN) ASIC, in turn, features a large one-dimensional systolic array of identical processing elements (PEs). The BioSCAN system scans approximately two million database elements per second. For typical problems this results in a 1000-fold speedup over current workstations

Keywords

VLSI; biology computing; computer architecture; database management systems; medical administrative data processing; microcomputers; special purpose computers; BioSCAN; DNA; VLSI-based system; biological sequence comparative analysis node; biosequence analysis; custom-designed circuit board; databases; full-custom ASICs; one-dimensional systolic array; processing elements; protein sequences; Acceleration; Application specific integrated circuits; Biology computing; DNA computing; Printed circuits; Proteins; Sequences; Spatial databases; Systolic arrays; Workstations;

fLanguage

English

Publisher

ieee

Conference_Titel

Computer Design: VLSI in Computers and Processors, 1991. ICCD '91. Proceedings, 1991 IEEE International Conference on

Conference_Location

Cambridge, MA

Print_ISBN

0-8186-2270-9

Type

conf

DOI

10.1109/ICCD.1991.139959

Filename

139959