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Hepatitis B virus (HBV) has evolved into phylogenetically separable genotypes and subgenotypes. Accurately assigning the subgenotype for an HBV strain is of clinical and epidemiological significance. In this paper, we review the recommendations currently employed for HBV subgenotyping, the history of HBV subgenotyping, the effects of recombination on HBV(More)
The Smith-Waterman (SW) algorithm is universally used for a database search owing to its high sensitively. The widespread impact of the algorithm is reflected in over 8000 citations that the algorithm has received in the past decades. However, the algorithm is prohibitively high in terms of time and space complexity, and so poses significant computational(More)
BACKGROUND More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist. METHODOLOGY/PRINCIPAL FINDINGS We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences(More)
We present a novel implementation of the pairwise DNA sequence alignment problem other than the Dynamic programming solution presented by Smith Waterman Algorithm. The proposed implementation uses CUDA; the parallel computing platform and programming model invented by NVIDIA. The main idea of the proposed implementation is assigning different nucleotide(More)
For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a(More)
MrBayes is model-based phylogenetic inference tool using Bayesian statistics. However, model-based assessment of phylogenetic trees adds to the computational burden of tree-searching, and so poses significant computational challenges. Graphics Processing Units (GPUs) have been proposed as high performance, low cost acceleration platforms and several(More)
Ming-Wei Lin,1 Cheng Ling,1 Luis A. Agapito,2 Nicholas Kioussis,2 Yiyang Zhang,1,3 Mark Ming-Cheng Cheng,3 Wei L. Wang,4 Efthimios Kaxiras,4 and Zhixian Zhou1,* 1Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA 2Department of Physics, California State University, Northridge, California 91330, USA 3Department of(More)