Computational protocol: Human rotavirus strains circulating in Venezuela after vaccine introduction: predominance of G2P[4] and reemergence of G1P[8]

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Protocol publication

[…] Alignment and comparison of nucleotide and deduced amino acid sequences of VP7 and VP4 genes from the selected Venezuelan RV isolates were performed by using BLAST® (Basic Local Alignment Search Tool) web service of U.S. National Library of Medicine (blast.ncbi.nlm.nih.gov), and ClustalW method. Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 6.06 []. The phylogenetic trees were generated by neighbor-joining method and with the Kimura’s two-parameter as substitution model, from nucleotide sequences of the RV strains in this study together with global reference strains available in the NCBI (National Center for Biotechnology Information) GenBank database (https://www.ncbi.nlm.nih.gov/nucleotide/) and Rotarix® vaccine strain. The statistical significance of the branches was assessed by bootstrap resampling analysis (1000 replicates). [...] A high-quality homology-based model from VP7 deduced amino acid sequences from G1P[8] strains from this study was generated automatically from the ModBase database by the ModWeb server version r181 from the University of California (San Francisco, USA) []. The models were built by using the crystal structure (Protein Data Bank identifier [PDB ID], 3FMG) of RV outer capsid protein VP7 trimer in complex with a neutralizing Fab as template []. Protein structural analysis and modeling were performed using the UCSF Chimera-Molecular Modeling System v1.11 (University of California, San Francisco) [], and the Adobe Illustrator CS6 software was utilized as a design tool of the image. […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA, ModWeb, UCSF Chimera, Adobe Illustrator
Databases ModBase
Applications Miscellaneous, Phylogenetics, Protein structure analysis
Organisms Homo sapiens
Diseases Coinfection
Chemicals Amino Acids