Computational protocol: Detection of HCV Persistent Infections in the Dental Pulp: A Novel Approach for the Detection of Past and Ancient Infections

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Protocol publication

[…] After molecular diagnosis of viral infection, positive samples were selected for amplification of the 5’UTR of HCV as previously described []. The product of the amplification was run on a 1.5% agarose gel stained with ethidium bromide and then visualized with ultraviolet light. The amplified fragment was sequenced in both directions according to Sanger et al. [] using an ABI Prism 310 Genetic Analyzer and the commercial kit Big Dye Cycle Sequencing Standard (Life Technologies, USA).Nucleotide sequences were edited and aligned using BioEdit software []. The final alignment was performed using Modelgenerator software [] aiming to select, according to the corrected Akaike information criterion, the best model to apply for the phylogenetic analysis. These parameters were used in the PHYML program version 2.4.4 [] to infer trees by the maximum-likelihood method. The statistical reliance of the tree topologies was evaluated using 1,000 bootstrap replicates.The final phylogenetic tree was obtained by majority-rule consensus and then edited using graphic resources found in the FigTree software []. Nucleotide sequences obtained from the National Center of Biotechnology Information were added to the alignment and used to construct the phylogenetic tree. The nucleotide sequence obtained in this study was deposited in the National Center of Biotechnology (#KU955710). […]

Pipeline specifications

Software tools BioEdit, ModelGenerator, PhyML, FigTree
Application Phylogenetics
Organisms Human poliovirus 1 Mahoney, Homo sapiens
Diseases Hepatitis C, Infection, HIV Infections
Chemicals Nitrogen