Computational protocol: The epitope regions of H1-subtype influenza A, with application to vaccine efficacy

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Protocol publication

[…] Three hundred and twenty H1N1 swine flu protein sequences as of 18 May 2009 were downloaded from the NCBI and GISAID databases. ClustalW is applied to align these strains. Two hundred and sixty-six sequences containing residues 27–324 (A/California/04/2009 numbering, modified from ) were used to create the phylogenic tree with PHYLIP (). Two hundred and sixty-six subsequences that included residues 27–324 were extracted, and duplicated subsequences were removed. The 23 unique aligned subsequences were then used as the input of the program PHYLIP. The distance matrix from protein sequences (protdist) and the Fitch–Margoliash and least squares methods with evolutionary clock (kitsch) () were sequentially applied to generate the phylogenic tree in Fig. . The output of protdist is the input of kitsch. In the phylogenetic tree, the strain A/California/07/2009 (FJ966974) is one of the outgroups, which are closest to the root. […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Sus scrofa, Homo sapiens
Diseases Influenza, Human