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Protocol publication

[…] ons., A single PCR assay was used to discriminate between the homB and homA genes (fragments of 161 bp and 128 bp, respectively) []. In order to study the diversity of homB and homA genes, PCR primers targeting a conserved region of the flanking genes of both loci jhp0649 and jhp0870, according to the numbering of the J99 strain [], were designed for amplification of the entire genes []. The fragments were subsequently sequenced using the PCR primers and internal primers, as previously described []., Similarity plots, using SimPlot Version 3.5.1, 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 [] 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 th […]

Pipeline specifications

Software tools BioEdit, Biotools, BioBin
Organisms Helicobacter pylori
Diseases Peptic Ulcer, Dyspepsia