Degree Type

Thesis

Date of Award

2012

Degree Name

Master of Science

Department

Electrical and Computer Engineering

First Advisor

Joseph Zambreno

Abstract

The alignment of many short sequences of DNA, called reads, to a long reference genome is a common task in molecular biology. When the problem is expanded to handle typical workloads of billions of reads, execution time becomes critical. While existing solutions attempt to align a high percentage of the reads using a small memory footprint, RAMPS (Reconfigurable Architecture for Minimal Perfect Sequencing) focuses on perform fast exact matching. Using the human genome as a reference, RAMPS aligns short reads on the order of hundreds of thousands of times faster than current software implementations such as SOAP2 or Bowtie, and about 1000 times faster than GPU implementations such as SOAP3. Whereas other aligners require hours to preprocess reference genomes, RAMPS can preprocess the human genome in a few minutes, opening doors via the ability to use arbitrary reference sources for alignment to increase the amount of data that exactly aligns with the reference.

Copyright Owner

Chad Michael Nelson

Language

en

File Format

application/pdf

File Size

49 pages

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