A scalable parallel reconfigurable hardware architecture for DNA matching

被引：3

作者：

Garcia Neto Segundo, Edgar Jose ^{[1
]}

Nedjah, Nadia ^{[1
]}

Mourelle, Luiza de Macedo ^{[2
]}

机构：

[1] Univ Estado Rio De Janeiro, Dept Elect Engn & Telecommun, Rio De Janeiro, Brazil

[2] Univ Estado Rio De Janeiro, Dept Syst Engn & Computat, Rio De Janeiro, Brazil

来源：

INTEGRATION-THE VLSI JOURNAL | 2013年 / 46卷 / 03期

关键词：

DNA alignment; DNA matching; Reconfigurable hardware; BLAST;

D O I：

10.1016/j.vlsi.2013.01.002

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

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 the 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. (c) 2013 Elsevier B.V. All rights reserved.

引用

页码：240 / 246

页数：7

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