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genoBASE pylori: a genotype search tool and database of the human gastric pathogen Helicobacter pylori

Ahmed, Niyaz and Majeed, Ahmed A. and Ahmed, Irshad and Hussain, M. Abid and Alvi, Ayesha and Devi, Sundru Manjulata and Rizwan, Mohammed and Ranjan, Akash and Sechi, Leonardo Antonio and Megraud, Francis (2007) genoBASE pylori: a genotype search tool and database of the human gastric pathogen Helicobacter pylori. Infection, Genetics and Evolution, Vol. 7 (4), p. 463-468. ISSN 1567-1348. Article.

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DOI: 10.1016/j.meegid.2007.01.006

Abstract

Helicobacter pylori is the pathogenic bacterium linked to gastric and duodenal ulcers and gastric carcinoma. Genomic diversity of the organism has enabled new insights into its population biology through comparative genomics. genoBASE pylori is an online databank of several virulence-linked and phylogenetic markers of H. pylori strains obtained from different human populations. This knowledgebase is built upon a relational database management system which is connected to visualize the presence of known, pathogenicity markers such as the co-ordinates within the cag pathogenicity island (cagPAI), the cagA gene and motifs surrounding it, the vacA allotypes and the oipA gene frame status, together with genotypic details in the form of DNA profiling traces and candidate gene sequences for individual strains. This flexible search tool allows inter-laboratory comparison of DNA fingerprinting data in the form of fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) signature profiles. Besides this, the database also displays diversity of strains based on nucleotide sequences of several house keeping genes and two membrane proteins. Being the first of its kind, genoBASE pylori is expected to be a helpful online tool in strengthening the concept of ‘geographic genomics’ and will be useful to molecular epidemiologists, clinical laboratory scientists and those interested in diagnostic development for H. pylori. The database can be accessed through its website (http://www.cdfd.org.in/amplibase/HP).

Item Type:Article
ID Code:3853
Status:Published
Refereed:Yes
Uncontrolled Keywords:H. pylori, strain databases, genotyping, pathogenesis, diagnostic markers, multilocus sequence typing, lineage identification, geographic genomics
Subjects:Area 06 - Scienze mediche > MED/07 Microbiologia e microbiologia clinica
Divisions:001 Università di Sassari > 01 Dipartimenti > Scienze biomediche
002 Altri enti e centri di ricerca del Nord Sardegna > ISOGEM-International Society for Genomic and Evolutionary Microbiology, Sassari
Publisher:Elsevier
ISSN:1567-1348
Deposited On:10 May 2010 11:32

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