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

Similar protocols

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 (, 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 ( 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