Go to the abstract in the NAR 2002 Database Issue.
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Harmsen, D.1, Rothgänger, J.2, Sammeth, M.2, Albert, J.2
1Institut für Hygiene, Universität Münster, D-48149 Münster, Germany
2Lehrstuhl für Informatik II, Universität Würzburg, D-97074 Würzburg, Germany
Contact dharmsen@ridom.de
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.
The RIDOM web-site will be re-launched with added functionality (e.g. simultaneous multiple alignment) and an extended database content end of the year 2002.
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.
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.
Harmsen,D., Rothgänger,J., Frosch,M. and Albert,J. (2002) RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Res., 30, 416-417.
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.
Category Varied Biomedical Content
Go to the abstract in the NAR 2002 Database Issue.