NAR Molecular Biology Database Collection entry number 299

http://www.ridom.de/

Harmsen, D.¹, Rothgänger, J.², Sammeth, M.³, Albert, J.⁴

¹Institut für Hygiene, Universität Münster, D-48149 Münster, Germany
²Ridom GmbH, D-97082 Würzburg, Germany
³Genome Informatics, Department of Technology, Universität Bielefeld, D-33594 Bielefeld, Germany
⁴Lehrstuhl für Informatik II, Universität Würzburg, D-97074 Würzburg, Germany

Contact rdna@ridom.de

The ribosomal differentiation of 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. 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-rdna.de/. The email address for questions and comments is webmaster@ridom-rdna.de.

Nocardia and Staphylococcus entries will be added soon.

Database Description

Harmsen,D., Rothgänger,J., Singer,C., Albert,J. and Frosch,M. (1999) Intuitive hypertext-based molecular identification of micro-organisms. Lancet 353: 291.
Harmsen,D., Singer,C., Rothgänger,J., Tønjum,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.
Harmsen,D., Rothgänger,J., Frosch,M. and Albert,J. (2002) RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Res. 30: 416-417.
Dostal,S., Richter,E. and Harmsen,D. (2003). Concise guide to mycobacteria and their molecular differentiation, p. 1-224. Ridom Press, Würzburg (Germany, ISBN 3-8330-0513-0).
Mellmann,A., Cloud,J.L., Andrees,S., Blackwood,K., Carroll,K.C., Kabani,A., Roth,A. and Harmsen,D. (2003). Evaluation of RIDOM, MicroSeq, and GenBank services in the molecular identification of Nocardia species. Int. J. Med. Microbiol. 292: (in press).

Database Evaluation

Turenne,C.Y., Tschetter,L., Wolfe,J. and Kabani,A. (2001) Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J. Clin. Microbiol. 39: 3637-3648.
Cloud,J.L., Neal,H., Rosenberry,R., Turenne,C.Y., Jama,M., Hillyard, D.R. and Carroll,K.C. (2002) Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J. Clin. Microbiol. 40: 400-406.
Hall,L., Doerr,K.A., Wohlfiel,S.L. and Roberts,G. (2003). Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J. Clin. Microbiol. 41: 1447-1453.
Tortoli,E. (2003). Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev. 16: 319-354.

Go to the abstract in the NAR 2002 Database Issue.

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