Acceleration of Gapped Alignment in BLASTP Using the Mercury System

Authors

Brandon B. Harris, Washington University in St Louis

Document Type

Technical Report

Department

Computer Science and Engineering

Publication Date

2006-01-01

Filename

wucse-2006-47.pdf

Technical Report Number

WUCSE-2006-47

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.

Comments

Permanent URL: http://dx.doi.org/10.7936/K7V40SD8

Recommended Citation

Harris, Brandon B., "Acceleration of Gapped Alignment in BLASTP Using the Mercury System" Report Number: WUCSE-2006-47 (2006). All Computer Science and Engineering Research.
https://openscholarship.wustl.edu/cse_research/197