Computational protocol: Study of Helicobacter pylori genotype status in cows, sheep, goats and human beings

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Protocol publication

[…] DNA sequencing analysis was performed on 6 H. pylori positive sample; 3 samples from cows and 3 samples from sheep which were selected randomly. Due to limitations we were not able to do sequence on all positive samples for glmM gene. For this purpose the DNA extraction was done by the same method as mentioned before for PCR. The amplified 296-bp PCR products (glmM gene) from 6 positive samples were purified with High pure PCR product purification kit (Roche Applied Science), according to manufacturer’s recommendations. Single DNA strands were sequenced with ABI 3730 XL device and Sanger sequencing method (Macrogen, Korea).After the sequence of 6 isolates were trimmed by using Edit View v.1.0.1 (Applied Bioscience, Australia), the sequences of 8 isolate with human source, which has been stored in GenBank with accession numbers: FN598874, CP003476, DQ462665, M60398, NC017361, GU445163, DQ141576, AB664954 were aligned separately against obtained animal isolate sequences using the Clustal W v1.81 in order to obtain a consensus sequence for the gene, glmM (H. pylori ureC). BioEdit Pakage V. was used to edit all sequence alignments. The nucleotide sequences of the Iranian ruminant H. pylori glmM (ureC) gene was compared with the correspond sequences reported from other regions via NCBI. By using Njplot software and 1000 bootstrap replicate, an unrooted dendrogramme was constructed. […]

Pipeline specifications

Software tools Clustal W, BioEdit, NJplot
Application Phylogenetics
Organisms Helicobacter pylori, Ovis aries, Capra hircus, Bos taurus, Homo sapiens
Diseases Gastrointestinal Diseases