Computational protocol: Antigenic Diversity of Human Sapoviruses

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Protocol publication

[…] Nucleotide sequences were determined by using the Terminator Cycle Sequence Kit version 3.1 and an ABI 3130 sequencer (both from Applied Biosytems, Boston, MA, USA). Nucleotide sequences were aligned with ClustalX (www.embl.de/~chenna/clustal/darwin) and the distances were calculated by the Kimura 2-parameter method (). Phylogenetic trees with bootstrap analysis from 1,000 replicas were generated by the neighbor-joining method as described (). Amino acid VP1 secondary structure predictions were made by using PSIPRED secondary structural prediction software (). […]

Pipeline specifications

Software tools Clustal W, PSIPRED
Application Phylogenetics
Organisms Homo sapiens, Great Island virus
Diseases Gastroenteritis