Computational protocol: Re-Emergence of Dengue Virus Type 3 in Canton, China, 2009–2010, Associated with Multiple Introductions through Different Geographical Routes

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Protocol publication

[…] Purified PCR products were directly sequenced in both forward and reverse directions using the same primers as for PCR using the ABI Prism® BigDye™ Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, USA) according to the manufacturer’s protocol. The nucleotide sequences were determined by ABI PRISM® 3700 Genetic Analyzer (Applied Biosystems). Sequences assemblies were completed using the SeqMan II software (DNASTAR, Inc., Madison, WI, USA) . The identity of nucleotide and amino acid sequences was determined by use of the BLAST engine (http://www.ncbi.nlm.nih.gov/Entrez/). Nucleotide sequences were aligned with the sequence alignment software Clustal X v.1.83 . The phylogenetic tree was constructed by the neighbour-joining methods with a Kimura 2 parameter model using MEGA 4.0 software (Molecular Evolutionary Genetics Analysis, Version 4.0) . Bootstrap analyses with 1,000 replicates were used to determine the robustness of the tree. DENV-1 (D1/USA/Hawaii/1945) strains (GenBank accession number: AF425619) was used as out-group to root the trees. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Dengue virus 3, Homo sapiens