Computational protocol: Genetic Diversity of Staphylocoagulase Genes (coa): Insight into the Evolution of Variable Chromosomal Virulence Factors in Staphylococcus aureus

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Protocol publication

[…] MLST was preformed as described previously . CC was determined by eBURST analysis . It was defined as a group in which the STs were identical in sequence at six of seven MLST genes (arcC, aroE, glpF, gmk, pta, tpi and yqiL) to at least one other ST in the group. [...] Genetic analysis was mainly carried out using programs in GENETYX-MAC Version 13.0.3 (GENETYX Corporation, Tokyo, Japan).The nucleotide sequences of coa or concatenated fragments of MLST genes were aligned using the clustalW Version 1.83 program with 1000 times bootstrapping and neighbor-joining analysis was carried out with Tajima-Nei parameter model. Phylogenetic trees were visualized with TreeView X program . Recombinations in and around coa were detected using the RDP3 Beta 34 software . We used six automated recombination detection methods, RDP , Geneconv , Bootscanning , Maximum Chi Square (MaxChi) , Chimaera , and Sister Scanning (SiScan) . Results were verified by visual inspection. […]

Pipeline specifications

Software tools BURST, Clustal W, TreeViewX
Applications Phylogenetics, WGS analysis
Organisms Staphylococcus aureus, Epipremnum aureum
Diseases Pierre Robin Syndrome, Blood Coagulation Disorders, Inherited