Chapter 13. GPU-Supercomputer Acceleration of Pattern Matching
Ali Khajeh-Saeed and J.Blair Perot
This chapter describes the solution of a single very large pattern-matching search using a supercomputing cluster of GPUs. The objective is to compare a query sequence that has a length on the order of
with a “database” sequence that has a size on the order of roughly
, and find the locations where the test sequence best matches parts of the database sequence. Finding the optimal matches that can account for gaps and mismatches in the sequences is a ...