Computational protocol: The molecular epidemiology of respiratory viruses associated with asthma attacks

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Protocol publication

[…] We performed phylogenetic analyses using Molecular Evolutionary Genetics Analysis (MEGA) software, version 5.0. Phylogenetic analysis of hMPV, RSV, and HRV was based on parts of the F gene (317 bp), G gene (240–312 bp on RSV-A, 234– 294 bp on RSV-B), and VP4/VP2 coding region (390 bp), respectively.The species of the viruses were estimated using the basic local alignment search tool (BLAST).[] Evolutionary distances were estimated using the Kimura 2-parameter method and phylogenetic trees were constructed using the neighbor-joining (NJ) method. Reliability of the trees was estimated using 1,000 bootstrap replications. We calculated pairwise distances (p-distance) of the respiratory viruses detected in this study, hMPV, RSV, Inf-V, and HRV, using MEGA software, version 5.0. Calculations were based on the nucleotide sequences of each virus. […]

Pipeline specifications

Software tools MEGA, BLASTN
Application Phylogenetics
Organisms Homo sapiens, Human metapneumovirus, Rous sarcoma virus
Diseases Asthma, Influenza, Human, Respiratory Tract Infections