Computational protocol: Identification of two mutation sites in spike and envelope proteins mediating optimal cellular infection of porcine epidemic diarrhea virus from different pathways

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Protocol publication

[…] The transmembrane domain of the PEDV E protein was predicted by TMHMM 2.0 []. The schematic overview of the PEDV S2 domain was referred to as the SARS-CoV and then drawn to scale []. The nucleotides (S gene or the whole genome of PEDV) or amino acid sequence alignments (S or E protein) were performed using ClustalW with default parameters, using reference sequences of strain DR13 (PEDV, JQ023161.1), cell-adapted DR13 (ca-DR13, JQ023162), strain CV777 (PEDV, AF353511), and strain Tor2 (SARS-CoV, NP828851.1). […]

Pipeline specifications

Software tools TMHMM, Clustal W
Application Membrane protein analysis
Organisms Porcine epidemic diarrhea virus, Human poliovirus 1 Mahoney
Diseases Infection, HIV Infections
Chemicals Glycine