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

Authors:
Jung-Yup Kang;Sandeep Gupta;Jean-Luc Gaudiot
Affiliations:
University of Southern California;University of Southern California;University of California at Irvine
Venue:
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Year:
2004

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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.