Computational protocol: Neutralising antibody response in domestic cats immunised with a commercial feline immunodeficiency virus (FIV) vaccine

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Protocol publication

[…] Twenty-four VR1012 plasmids expressing SV1 FIV envs were sequenced using the Big Dye Terminator v1.1 kit. The full length FIV env sequence (approx. 2500 bp) from each clone was assembled using 4 sequencing reads overlapping by approximately 200 bp and manually checked for mismatches. Nucleotide and peptide sequence alignment was performed using the Muscle algorithm in MEGA5 . Evolutionary divergence between sequences was calculated using the Maximum Composite Likelihood model . A phylogenetic tree comprising the complete env sequences was constructed using the maximum likelihood (ML) method under HKY nucleotide substitution model in MEGA5. Sequences were analysed using the Datamonkey webserver , employing the genetic algorithm recombination detection (GARD) method . Neighbour joining (NJ) trees for each recombination segment (identified by GARD and assessed by Akaike Information Criterion (AIC) ) were prepared for presentation in FigTree v 1.3.1 ( A representative figure visualizing recombination breakpoints was generated in SimPlot v 3.5.1 . Highlighter analysis was performed using the highlighter tool available at the Los Alamos National Laboratory server ( Graphs were created in GraphPad Prism v 5.00 (GraphPad Software). […]

Pipeline specifications

Software tools MUSCLE, MEGA, Datamonkey, GARD, FigTree, SimPlot
Applications Phylogenetics, Population genetic analysis, Nucleotide sequence alignment
Organisms Felis catus, Homo sapiens, Feline immunodeficiency virus
Diseases Immunologic Deficiency Syndromes, Infection, Leukemia, HIV Infections