RAPID GENOME ANALYSIS ON A WORKSTATION WITH AN ASSOCIATIVE COPROCESSOR

THE GOAL OF THIS RESEARCH IS TO PRODUCE A HIGH PERFORMANCE, LOW COST SEQUENCE ANALYSIS WORKSTATION THAT WILL ALLOW GENETIC RESEARCHERS TO PERFORM COMPLEX ANALYSES ON GENOME DATA. PHASE I STUDIES THE FEASIBILITY OF PROCESSING GENOME DATA AT THE WORKSTATION WITH AN ASSOCIATIVE COPROCESSOR. MANY OF THE ANALYSES OF DNA SEQUENCES REQUIREDBY MOLECULAR BIOLOGIST INVOLVE FINDING SIMILARITIES BETWEEN DIFFERENT MOLECULES OR WITHIN ONE MOLECULE. SEVERAL DIFFERENT APPROACHES WITHIN DOZENS OF PROGRAMS HAVE BEEN APPLIED TO THIS PROBLEM. WITH INCREASING SEQUENCE LENGTH (OR LARGER NUMBERS OF FRAGMENTS), THESE METHODS CAN QUICKLY BECOME COMPUTATIONALLY IMPRACTICAL. THE AVAILABILITY OF RECENT PARALLEL PROCESSORS PROVIDES AN AVENUE FOR SPEEDING UP SEQUENCE ANALYSIS. BY IMPLEMENTING A SIMPLIFIED COMPUTATIONAL MODEL USING VERY LARGE SCALE INTEGRATION (VLSI), THE ASSOCIATIVE PROCESSOR-DEVELOPMENT SYSTEM (AP-DS)PROVIDES THE SAME DEGREE OF PARALLEL PROCESSING AS EITHER THE CONNECTION MACHINE OR THE DISTRIBUTED ARRAY PROCESSOR ATA MUCH LOWER COST. THIS RESEARCH WILL SHOW THE FEASIBILITY OF PROCESSING COMPLEX GENOME QUERIES ON A WORKSTATION-CLASS MACHINE WITH AN ATTACHED AP-DS COPROCESSOR.