BioSCAN: a VLSI-based system for biosequence analysis
C.T. White, Raj K. Singh, Peter B. Reintjes, Johanna W. Lampe, B W Erickson, W.D. Dettloff, V.L. Chi, Stephen F. Altschul · 2002
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.>