Acceleration of Gapped Alignment in BLASTP Using the Mercury System

Abstract

Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results. 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 Acceleration of Gapped Alignment in BLASTP Using the Mercury System Brandon Harris bbh2@wustl.edu Abstract Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results.Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results.

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Cite this paper

@inproceedings{Harris2016AccelerationOG, title={Acceleration of Gapped Alignment in BLASTP Using the Mercury System}, author={Brandon Harris}, year={2016} }