probeBase - An online resource for rRNA-targeted oligonucleotide probes: New features 2007

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Loy, Alexander ^a   Maixner, Frank ^a   Wagner, Michael ^a   Horn, Matthias ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER MODEL; E-MAIL; ERROR; GENETIC DATABASE; IN SITU HYBRIDIZATION; INTERNET; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE PROBE; ONLINE SYSTEM; PRIORITY JOURNAL; PROBEBASE; PUBLICATION; RNA PROBE; RNA SEQUENCE;

BACTERIA; DATABASES, NUCLEIC ACID; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33846102841     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl856     Document Type: Article

References (27)

1. Amann,R., Fuchs,B.M. and Behrens,S. (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotechnol., 12, 231-236.
2. Loy,A. and Bodrossy,L. (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta, 363, 106-119.
3. Wagner,M., Horn,M. and Daims,H. (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr. Opin. Microbiol., 6, 302-309.
4. Daims,H., Lücker,S. and Wagner,M. (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol., 8, 200-213.
5. Wagner,M., Nielsen,P.H., Loy,A., Nielsen,J.L. and Daims,H. (2006) Linking microbial community structure with function: Fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr. Opin. Biotechnol., 17, 1-9.
6. Galperin,M.Y. (2006) The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res., 34, D3-D5.
7. Loy,A., Horn,M. and Wagner,M. (2003) probeBase: An online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res., 31, 514-516.
8. Daims,H., Brühl,A., Amann,R., Schleifer,K.-H. and Wagner,M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol., 22, 434-444.
9. Loy,A., Schulz,C., Lücker,S., Schöpfer-Wendels,A., Stoecker,K., Baranyi,C., Lehner,A. and Wagner,M. (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl. Environ. Microbiol., 71, 1373-1386.
10. Yilmaz,L.S., Oklen,H.E. and Noguera,D.R. (2006) Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl. Environ. Microbiol., 72, 733-744.
11. Yilmaz,L.S. and Noguera,D.R. (2004) Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Appl. Environ. Microbiol., 70, 7126-7139.
12. Cole,J.R., Chai,B., Farris,R.J., Wang,Q., Kulam,S.A., McGarrell,D.M., Garrity,G.M. and Tiedje,JM. (2005) The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33, 294-296.
13. DeSantis,TZ, Hugenholtz,P., Larsen,N., Rojas,M., Brodie,E.L., Keller,K., Huber,T., Dalevi,D., Hu,P. and Andersen,G.L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
14. Ludwig,W., Strunk,O., Westram,R., Richter,L., Meier,H., Yadhukumar, Buchner,A., Lai,T., Steppi,S., Jobb,G. et al. (2004) ARB: A software environment for sequence data. Nucleic Acids Res., 32, 1363-1371.
15. Behrens,S., Ruhland,C., Inacio,J., Huber,H., Fonseca,A., Spencer-Martins,I., Fuchs,B.M. and Amann,R. (2003) In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl. Environ. Microbiol., 69, 1748-1758.
16. Zheng,D., Alm,E.W., Stahl,D.A. and Raskin,L. (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol., 62, 4504-4513.
17. Amann,R.I., Binder,B.J., Olson,R.J., Chisholm,S.W., Devereux,R. and Stahl,D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol., 56, 1919-1925.
18. Neef,A. (1997) Ph. D. thesis. Anwendung der in situ Einzelzell-Identifizierung von Bakterien zur Populations analyse in komplexen mikrobiellen Biozönosen. Technische Universität München, München.
19. Loy,A., Lehner,A., Lee,N., Adamczyk,J., Meier,H., Ernst,J., Schleifer,K.-H. and Wagner,M. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol., 68, 5064-5081.
20. Schönhuber,W., Zarda,B., Eix,S., Rippka,R., Herdman,M., Ludwig,W. and Amann,R. (1999) In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol., 65, 1259-1267.
21. Weller,R., Glöckner,F.O. and Amann,R. (2000) 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Syst. Appl. Microbiol., 23, 107-114.
22. Gich,F., Garcia-Gil,J. and Overmann,J. (2001) Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch. Microbiol., 177, 1-10.
23. Tuschak,C., Glaeser,J. and Overmann,J. (1999) Specific detection of green sulfur bacteria by in situ hybridization with a fluorescently labeled oligonucleotide probe. Arch. Microbiol., 171, 265-272.
24. Neef,A., Amann,R., Schlesner,H. and Schleifer,K.-H. (1998) Monitoring a widespread bacterial group: In situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology, 144, 3257-3266.
25. Poppert,S., Essig,A., Marre,R., Wagner,M. and Horn,M. (2002) Detection and differentiation of chlamydiae by fluorescence in situ hybridization. Appl. Environ. Microbiol., 68, 4081-4089.
26. Juretschko,S., Loy,A., Lehner,A. and Wagner,M. (2002) The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol., 25, 84-99.
27. Hugenholtz,P., Tyson,G.W., Webb,R.I., Wagner,A.M. and Blackall,L.L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl. Environ. Microbiol., 67, 411-419.