A scalable parallel reconfigurable hardware architecture for DNA matching

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.

► Efficient Parallel implementation of BLAST on FPGA-based hardware.
► Scalable design in terms of characteristics of the DNA sequences.
► Average performance speedup of 60× of the proposed hardware over the software-based implementation.