Computational protocol: The prevalence of the duodenal ulcer promoting gene (dupA) in Helicobacter pylori isolates varies by ethnic group and is not universally associated with disease development: a case-control study

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Protocol publication

[…] 29 single colony isolates (4 Chinese, 2 Indian, 4 Malay, 3 Australian and 3 Swedish FD isolates, 4 Chinese and 3 Swedish DU isolates, and 3 Chinese and 3 Swedish GC isolates) were sequenced to validate the specificity of the primers dupA F and dupA R and to ascertain whether JHP0917-0918 formed a single continuous gene in these isolates. Sequencing was performed using the BigDye™ Terminator version 3.1 (Applied Biosystems, Foster City, California, USA). Sequencing analysis was performed on an ABI3730 Capillary DNA sequencer (GENterprise, Mainz, Germany). Sequences were verified using Blast [] available from Biomanager by ANGIS . Sequence alignments of the 29 strains, with the original dupA gene sequence from Gene Bank (accession no. AB196363) [] and two additional dupA-like sequences (accession no. EF076755 and EF076756) available in the GenBank database were created using ClustalW accurate [] also available from BioManager. […]

Pipeline specifications

Software tools BioManager, Clustal W
Application Miscellaneous
Organisms Helicobacter pylori, Homo sapiens, Martes pennanti
Diseases Stomach Neoplasms