Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master's Thesis

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. Mercury BLAST makes use of new algorithms combined with reconfigurable hardware to accelerate BLAST-like similarity search. An evaluation of this method for use in real BLAST-like searches is presented along with a characterization of the quality of results associated with using these new algorithms in specialized hardware. The primary focus of this thesis is the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and performs over 20× faster than that of the standard software Type of Report: Other Department of Computer Science & Engineering Washington University in St. Louis Campus Box 1045 St. Louis, MO 63130 ph: (314) 935-6160 WASHINGTON UNIVERSITY THE HENRY EDWIN SEVER GRADUATE SCHOOL DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING DESIGN AND EVALUATION OF A BLAST UNGAPPED EXTENSION ACCELERATOR by Joseph M. Lancaster Prepared under the direction of Jeremy Buhler and Roger Chamberlain A thesis presented to the Henry Edwin Sever Graduate School of Washington University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 2006 Saint Louis, Missouri WASHINGTON UNIVERSITY THE HENRY EDWIN SEVER GRADUATE SCHOOL DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING