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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)
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)
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)
Dear Editor, The spread of the emerging zoonotic arboviral agent, Zika virus (ZIKV), in the Americas and its association with congenital abnormalities, 1,2 including in utero growth restriction, placental insuffi-ciency, microcephaly and fetal death, as well as neurological conditions, such as Guillain Barré syndrome, has led the World Health Organization(More)
This paper presents the design and implementation of the computationally intensive Smith Waterman and Needleman-Wunsch algorithms on the Virtex-5 (XC5VLX110) FPGA (Field Programmable Gate Array). A parameterisable architecture of the processing element (PE) for the pairwise biological sequence analysis is presented. We evaluate our core's performance in(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)