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 B9780123849885000139/si1.gif is missing with a “database” sequence that has a size on the order of roughly B9780123849885000139/si2.gif is missing, 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 ...

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