Computational protocol: Allelic diversity and phylogeny of homB, a novel co virulence marker of Helicobacter pylori

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Protocol publication

[…] Similarity plots, using SimPlot Version 3.5.1 http://sray.med.som.jhmi.edu/SCRoftware, were based on multiple alignments of the full nucleotide sequences of homB and homA genes generated by the BioEdit Sequence Alignment Editor (Version 7.0.1) []. Nucleotide sequences were translated using Translate Nucleic Acid Sequences software []http://biotools.umassmed.edu/cgi-bin/biobin/transeq. Neighbor-joining phylogenetic tree topologies of nucleotide and predicted amino acid alignments were constructed using the MEGA (Molecular Evolutionary Genetics Analysis) 3.1 software [], on the basis of distances estimated using the Kimura two-parameter model []. This model corrects for multiple hits, taking into account transitional and transversional substitution rates. Branching significance was estimated using bootstrap confidence levels by randomly resampling the data 1000 times with the referred evolutionary distance model. Evolutionary parameters were determined using MEGA 3.1. Mean molecular distances were determined using the Kimura two-parameter method [], while the overall mean of Ks and Ka substitutions were determined using the Nei-Gojobori method []. The standard error (SE) was determined for each parameter. A sliding window analysis of Ka and Ka/Ks ratio was performed using Swaap 1.0.2 software (Pride, D. T. (2000) Swaap - a tool for analyzing substitutions and similarity in multiple alignments). Due to the existence of alignment gaps, the complete-deletion option was used for all statistical analyses to normalize the number of differences on the basis of the number of valid sites compared. Bootstrap confidence levels were determined by randomly resampling the sequencing data 1000 times. The Codon Based Z-Test of selection [] was used to evaluate the significance of the values for the ratio of non-synonymous to synonymous substitutions. […]

Pipeline specifications

Software tools SimPlot, BioEdit, Biotools, BioBin, MEGA
Applications Phylogenetics, Population genetic analysis, GWAS
Organisms Helicobacter pylori
Diseases Dyspepsia, Peptic Ulcer