Computational protocol: Polymorphic genetic characterization of the ORF7 gene of porcine reproductive and respiratory syndrome virus (PRRSV) in China

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Protocol publication

[…] Sequence analysis of the partial Nsp2 gene and the complete ORF7 gene from all 7 isolates found in this study, in addition to 93 reference isolates from GenBank (Table ), was conducted using the Lasergene sequence analysis software package (DNASTAR Inc., Madison, WI). The CLUSTAL W program was used for multiple sequence alignment. The unrooted phylogenetic tree was generated by the distance-based neighbor-joining method using MEGA 4.0. Boot-strap values were calculated using 1000 replicates of the alignment. A hydrophilicity profile was generated with the ProtScale web utility http://expasy.org/tools/protscale.html by the Kyte and Doolittle method. Furthermore, the amino acid position was plotted versus the difference between non-synonymous and synonymous substitution rates (dN-dS). The difference was calculated with the SNAP web utility http://hiv-web.lanl.gov/content/hiv-db/SNAP/WEBSNAP/SNAP.html. […]

Pipeline specifications

Software tools Clustal W, ProtScale
Databases ExPASy
Applications Phylogenetics, Protein sequence analysis
Organisms Porcine reproductive and respiratory syndrome virus
Diseases Porcine Reproductive and Respiratory Syndrome