<abstract xmlns="http://www.w3.org/1999/xhtml"><p>With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays) technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation) errors.</p></abstract>

With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays) technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation) errors.

Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

Wigner Institute and Eötvös Loránd University

Acta Universitatis Sapientiae, Informatica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The...

Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

Published Online: Jan 22, 2016

Page range: 151 - 185

Received: Sep 15, 2015

Accepted: Dec 22, 2015

DOI: https://doi.org/10.1515/ausi-2015-0017

© 2015 Péter Fehér et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.