A scalable parallel reconfigurable hardware architecture for DNA matching

Author

Segundo, E.J.N. ; Nedjah, Nadia ; de Macedo Mourelle, Luiza

Author_Institution

Dept. Electron. Eng. & Telec., State Univ. of Rio de Janeiro, Rio de Janeiro, Brazil

fYear

2013

fDate

Feb. 27 2013-March 1 2013

Firstpage

1

Lastpage

4

Abstract

DNA sequence matching is used in the identification of a relationship between a fragment of DNA and its owner by mean of a database of DNA registers. A DNA fragment could be a hair sample left at a crime scene by a suspect or provided by a person for a paternity exam. The process of aligning and matching DNA sequences is a computationally demanding process. In this paper, we propose a novel parallel hardware architecture for DNA matching based on the steps of the BLAST algorithm. The design is scalable so that its structure can be adjusted depending on size of the subject and query DNA sequences. Moreover, the number of units used to perform in parallel can also be scaled depending some characteristics of the algorithm. The design was synthesized and programmed into FPGA. The trade-off between cost and performance were analyzed to evaluate different design configuration.

Keywords

DNA; bioinformatics; biological techniques; field programmable gate arrays; molecular biophysics; reconfigurable architectures; BLAST algorithm; DNA sequence aligning; DNA sequence matching; FPGA; bioinformatics; design configuration; scalable parallel reconfigurable hardware architecture; Algorithm design and analysis; Bioinformatics; DNA; Field programmable gate arrays; Hardware; Registers;

fLanguage

English

Publisher

ieee

Conference_Titel

Circuits and Systems (LASCAS), 2013 IEEE Fourth Latin American Symposium on

Conference_Location

Cusco

Print_ISBN

978-1-4673-4897-3

Type

conf

DOI

10.1109/LASCAS.2013.6518990

Filename

6518990