Second generation biological signal processor. Final progress report, February 15, 1993--February 14, 1995

The Biological Information Signal Processor (BISP) is a VLSI ASIC implementation of the dynamic programming methods favored for direct sequence-to-sequence comparison in order to discover local as well as global similarities. These methods, based on the local algorithm of Smith and Waterman provide the most mathematically robust solution to the problem of sequence alignment (determination of the optimal character-to-character registration between the two sequence, including relative insertions and deletions, indels). BISP provides a complete implementation of the standard Smith and Waterman algorithm in a systolic array that allows full parameterization and several novel extensions to the algorithm. BISP operates at supercomputer speeds from a VME board on a Sun workstation. Each VME array provides a complete systolic pipeline for comparison and multiple arrays can be combined linearly in order to increase the pipeline length. Overall performance is a function of the IO speed of the pipelined disk-resident data and the length of the array