Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: Now and next
| Autor: | Thomas Weniger, Justina Krawczyk, Philip Supply, Dag Harmsen, Stefan Niemann |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
DNA
Bacterial Microbiology (medical) Genotype Lineage (evolution) Minisatellite Repeats Computational biology Biology Multiple Loci VNTR Analysis Microbiology 03 medical and health sciences Genetics Data Mining Humans Tuberculosis Typing Molecular Biology Genotyping Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology Internet 0303 health sciences Phylogenetic tree 030306 microbiology Computational Biology Mycobacterium tuberculosis Molecular diagnostics biology.organism_classification Bacterial Typing Techniques 3. Good health Variable number tandem repeat Infectious Diseases Mycobacterium tuberculosis complex Databases Nucleic Acid Software Multilocus Sequence Typing |
| Zdroj: | Infection, Genetics and Evolution; Vol 12 |
| ISSN: | 1567-1348 |
| Popis: | Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 ( http://www.pasteur-guadeloupe.fr:8081/SITVITDemo ) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application ( http://www.miru-vntrplus.org ), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15-9 type) service that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions. Perspectives for future development, including generalization to other bacterial species, are presented. |
| Databáze: | OpenAIRE |
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