A 50MHz 1.5M Transistor ASIC For Biosequence Analysis

Identification and characterization of biological sequences are fundamental tasks of modern molecular biology. A major problem is to find biologically-significant methods for efficiently searching the large and rapidly-expanding DNA and protein sequence databases. One goal of the national Human Genome Initiative is to determine and analyze approximately 3 billion elements of human DNA sequence in the next 10 to 15 years. The BioSCAN chip implements the basic function central to several widely-used sequence analysis algorithms.1 A one-dimensional systolic array of 2,196 processing elements per chip covers over 90% of the area of this 1.5-milliontransistor ASIC.2