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Ribosomal Differentiation of Medical Microorganisms (RIDOM)

http://www.ridom.de/

Harmsen, D.¹, Rothg‰nger, J.², Frosch, M.¹, Albert, J.²

¹Institut f¸r Hygiene und Mikrobiologie, Universit‰t W¸rzburg, D-97080 W¸rzburg, Germany
²Lehrstuhl f¸r Informatik II, Universit‰t W¸rzburg, D-97074 W¸rzburg, Germany

Contact   dharmsen@ridom.de

Database Description

The ribosomal differentiation of medical microorganisms (RIDOM) web server, first described by Harmsen et al. [Lancet (1999), 353, 291] is an evolving electronic resource designed to provide microorganism differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit ribosomal DNA (16S rDNA) sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular, i.e. internal transcribed spacer (ITS), and conventional phenotypic differentiation will be offered ('sequential and polyphasic approach'). Additionally, each entry in RIDOM contains detailed medical and taxonomic information linked context-sensitive to external WWW services. Nearly all sequences are newly determined and the sequence chromatograms are available for intersubjective quality control. RIDOM currently contains 235 entries belonging to the Neisseriaceae, Moraxellaceae and Mycobacterium genus. A constant increase in the number of curated data is under development and periodic updates are planned. Similarity searches are possible by direct submission of trace files (ABI or SCF format). Based on the PHRED/PHRAP software, error probability measures are attached to each predicted nucleotide base and visualised with a 'Trace Editor'. The RIDOM web site is directly accessible on the WWW at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de.

Recent Developments

Trace file (ABI or SCF format) submission for similarity search conduction and trace editor.

REFERENCES

1. Harmsen,D., Rothg‰nger,J., Singer,C., Albert,J. and Frosch,M. (1999) Intuitive hypertext-based molecular identification of micro-organisms. Lancet, 353, 291.
2. Harmsen,D., Singer,C., Rothg‰nger,J., T¯njum,T., de Hoog,G.S., Shah,H., Albert,J. and Frosch,M. (2001) Diagnostics of Neisseriaceae and Moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical micro-organisms. J. Clin. Microbiol., 39, 936-942.

Category   Varied Biomedical Content

Go to the abstract in the NAR 2002 Database Issue.