WSEAS Transactions on Biology and Biomedicine
Print ISSN: 1109-9518, E-ISSN: 2224-2902
Volume 9, 2012
Identification of DNA Signatures via Suffix Tree Construction on a Hybrid Computing System
Authors: , , ,
Abstract: Identification of DNA signatures has been empowered by the increasing availability of thousands of bacterial and viral genomes through the next-generation sequencing technologies. In exploration for the computational solution, the suffix tree has been proposed as a data structure well suited to analyzing genomic sequences because it enables the storage of long strings in a logical, indexed manner for fast retrieval. We propose a new algorithm for identification of DNA signatures, based on exploitation of the endogenous features of a genomic sequence. These features are revealed in a construction of suffix array. Furthermore, to greatly speed up the time-consuming process, the core algorithm is mapped and routed on to a Field-Programable Gate Array (FPGA) for parallel implementation. In this paper, we will focus primarily on the relationship of the data structure and the features associated. We will then describe the deployment of the hybrid computing system on a HyperTransport compliant architecture. Illustrations are always given to clarify the technical details, and experimental results are presented to verify the correctness of the algorithm.
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Keywords: DNA signature, endogenous feature, suffix tree, Field-Programable Gate Array, hybrid computing