Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture

Jung-Yup Kang; Sandeep Gupta; Jean-Luc Gaudiot

doi:10.1109/CSB.2004.1332492

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Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference

Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture

Year: 2004, Pages: 552-553

DOI Bookmark: 10.1109/CSB.2004.1332492

Authors

Jung-Yup Kang, University of Southern California
Sandeep Gupta, University of Southern California
Jean-Luc Gaudiot, University of California at Irvine

Abstract

BLAST is a widely used tool to search for similarities in protein and DNA sequences. However, the kernels of BLAST are not efficiently supported by general-purpose processors because of the special computational requirements of the kernels.