Computational protocol: Genetic characterization of Chikungunya virus 2009 isolates from South India

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[…] From GenBank database, (n=360 sequences) CHIKV sequences were retrieved (DOA: 24/02/2016) and analysed along with study sequence. E2 gene was taken for analysis along with our sequences. Sequences were categorized based on the year of isolation, continent and genotypes. Likelihood mapping analysis was done to avoid the false conclusion about evolutionary relationships among strains using MEGA 7 []. Consensus was made for each category using codon code aligner (Tamura, Stecher et al. 2013). [...] The nucleotide sequences (n=37) were aligned using HyPhy package implemented in Datamonkey server [] and checked for redundancy. The potential recombination in the dataset was screened using GARD method. The selection pressure in the nucleotide sequence alignment was assessed using Parris method. The specific site selection on the gene was analysed using Single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), random effects likelihood (REL), MEME and fast-unconstrained bayesian approximation (FUBAR) algorithm. Positive selection was defined as p-value ≤ 0.1 for SLAC, FEL and Posterior probability ≥ 0.9 for FUBAR. [...] The secondary structure of the protein was predicted by PDBSUM []. The entire protein structure was unavailable in PDB; an ab-initio structure prediction was carried out using ITASSER []. The best model was selected using confidence score (C-score) and validated using Ramachandran plot predicted by SAVES server []. The substitutions reported in all the study isolates were modelled using Swiss PDB viewer []. All the structures were optimized using Gromacs 4.5.6 []. The structural consequences were investigated by comparing the wild type and mutant protein structures. The structures were visualized using PyMol. Changes in the intra-molecular interactions were analysed using PIC server []. […]

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