Nucleic Acids Research, 2000, Vol. 28, No. 1 175-176
© 2000 Oxford University Press
The European Small Subunit Ribosomal RNA database
Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium
Received October 4, 1999; Accepted October 6, 1999.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONTHE SSU rRNA DATABASESUPPLEMENTARY MATERIALREFERENCES |
|---|
The European database of the Small Subunit (SSU) Ribosomal RNA is a curated database that strives to collect all information about the primary and secondary structure of completely or nearly-completely sequenced rRNAs. Furthermore, the database compiles additional information such as literature references and taxonomic status of the organism the sequence was derived from. The database can be consulted via the WWW at URL http://rrna.uia.ac.be/ssu/ . Through the WWW, sequences can be easily selected either one by one, by taxonomic group, or by a combination of both, and can be retrieved in different sequence and alignment formats.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONTHE SSU rRNA DATABASESUPPLEMENTARY MATERIALREFERENCES |
|---|
Due to specific characteristics such as its ubiquity, size and low evolutionary rate, the small subunit ribosomal RNA (SSU rRNA) has proven to be an invaluable tool in molecular phylogenetic studies. The molecule has accounted for numerous new insights in evolutionary biology and its impact on our understanding of the origin and diversity of both prokaryotes and eukaryotes has been tremendous (1–3). Because of its popularity as a molecular marker, many thousands of complete or nearly complete SSU rRNA sequences are available now, from thousands of different species. Hence, a coherent and curated database is an incomparable tool for many areas of comparative biology, a role for which the SSU rRNA is still uniquely suited. The extent of the rRNA sequence collection is still far and away unrivaled among other molecular markers and constitutes by far the single most comprehensive database available for large-scale phylogenetic studies, and will undoubtedly remain so for a long time.
Although the SSU rRNA has been used primarily as a molecular marker in phylogenetic studies, it has also been the subject of many structural and functional studies. As a result, the secondary structure of both prokaryotic and eukaryotic rRNAs is now well resolved (4,5) and several functional domains have been identified and described (6,7).
|
THE SSU rRNA DATABASE |
|---|
|
TOPABSTRACTINTRODUCTIONTHE SSU rRNA DATABASESUPPLEMENTARY MATERIALREFERENCES |
|---|
The SSU rRNA database, housed in Antwerp, Belgium, is continuously updated by scanning the international nucleotide sequence libraries such as GenBank (8) and EMBL (9) for corrected or newly determined ribosomal RNA sequences. In general, only complete or nearly complete sequences are compiled. Partial SSU rRNA sequences are included in the database only if the combined length of the sequenced segments amounts to at least 70% of the estimated chain length of the molecule. The chain length of a partially determined sequence is estimated by comparing it to a complete sequence of a presumed close relative. All SSU rRNA sequences are stored in the form of an alignment and contain the postulated secondary structure pattern in encoded form. The SSU rRNA sequence alignment is based on two different secondary structure models. The first is the prokaryotic model (4,5), which is applicable to bacteria, Archaea, plastids and mitochondria, while the second is the eukaryotic model, applicable to all Eukaryotes (5). The two models are slightly different, each containing a number of structural elements specific for the group.
The SSU rRNA database is made available via the WWW at URL http://rrna.uia.ac.be/ssu/ . In order to simplify access to the Web data, each SSU rRNA sequence is stored in a separate file. Each of these files contains primary and secondary structure information, as well as annotations such as accession number, literature reference, and detailed taxonomic specifications. From January 2000 onwards, taxonomic specifications will be the same as those used by EMBL and GenBank, contrary to taxonomic descriptions used in previous releases of the SSU rRNA database (10).
Supplementary information available on line includes:
• detailed secondary structure models of prokaryotic, eukaryotic, plastidial and mitochondrial rRNAs
• nucleotide variability maps of the prokaryotic and eukaryotic SSU rRNA
Additional information directly available online on our server in Antwerp includes:
• information about the current status of the database
• taxonomic and alphabetic lists of prokaryotic and eukaryotic taxa represented in the database
• information about primers for sequencing SSU rRNA sequences
• phylogenetic trees of prokaryotes and eukaryotes
• software available for sequence alignment, tree construction and sequence alignment format conversion
• links to other relevant databases and resources
If problems occur in connecting to the server or in retrieving data, the authors can be contacted by Email to yves.vandepeer@uni-konstanz.de or dwachter@uia.ua.ac.be Users publishing results based on data retrieved from our database are requested to cite this paper.
|
SUPPLEMENTARY MATERIAL |
|---|
|
TOPABSTRACTINTRODUCTIONTHE SSU rRNA DATABASESUPPLEMENTARY MATERIALREFERENCES |
|---|
See Supplementary material available at NAR Online.
|
ACKNOWLEDGEMENTS |
|---|
Our research is supported by the Fund for Scientific Research (Flanders), by the Special Research Fund of the University of Antwerp (Belgium) and by the Faculty of Biology (Dr Axel Meyer) of the University of Konstanz. Y.V. de P. and P.De R. are Research Fellows of the Fund for Scientific Research (Flanders).
|
FOOTNOTES |
|---|
* To whom correspondence should be addressed. Tel: +32 3 820 2319; Fax: +32 3 820 2248; Email: dwachter@uia.ua.ac.be Present address: Yves Van de Peer, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONTHE SSU rRNA DATABASESUPPLEMENTARY MATERIALREFERENCES |
|---|
-
1 Olsen,G.J. and Woese,C.R. (1993) FASEB J., 7, 113–123.[Abstract]
2 Doolittle,W.F. and Brown,J.R. (1994) Proc. Natl Acad. Sci. USA, 91, 6721–6728.
3 Van de Peer,Y. and De Wachter,R. (1997) J. Mol. Evol., 45, 619–630.[Web of Science][Medline]
4 Gutell,R.R. (1994) Nucleic Acids Res., 22, 3502–3507.
5 Van de Peer,Y., Jansen,J., De Rijk,P. and De Wachter,R. (1997) Nucleic Acids Res., 25, 111–116.
6 Tapprich,W.E., Goss,D.J. and Dahlberg,A.E. (1989) Proc. Natl Acad. Sci. USA, 86, 4927–4931.
7 Noller,H.F., Moazed,D., Stern,S., Powers,T., Allen,P.N., Robertson,J.M., Weiser,B. and Triman,K. (1990) In Hill,W.E., Dahlberg,A., Garrett,R.A., Moore,P.B., Schlessinger,D. and Warner,J.R. (eds), The Ribosome. Structure, Function, and Evolution. American Society of Microbiology, Washington, DC, pp. 73–92.
8 Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J., Ouellette,B.F.F., Rapp,B.A. and Wheeler,D.L. (1999) Nucleic Acids Res., 27, 12–17. Updated article in this issue: Nucleic Acids Res. (2000), 28, 15–18.
9 Stoesser,G., Tuli,M.A., Lopez,R. and Sterk,P. (1999) Nucleic Acids Res., 27, 18–24. Updated article in this issue: Nucleic Acids Res. (2000), 28, 19–23.
10 Van de Peer,Y., Robbrecht,E., de Hoog,S., Caers,A., De Rijk,P. and De Wachter,R. (1999) Nucleic Acids Res., 27, 179–183.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  O. I. Nedashkovskaya, M. Suzuki, J.-S. Lee, K. C. Lee, L. S. Shevchenko, and V. V. Mikhailov Pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae, isolated from the green alga Ulva fenestrata Int J Syst Evol Microbiol, April 1, 2009; 59(4): 806 - 810. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, S. B. Kim, and V. V. Mikhailov Kriegella aquimaris gen. nov., sp. nov., isolated from marine environments Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2624 - 2628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Endo and S. Okada Reclassification of the genus Leuconostoc and proposals of Fructobacillus fructosus gen. nov., comb. nov., Fructobacillus durionis comb. nov., Fructobacillus ficulneus comb. nov. and Fructobacillus pseudoficulneus comb. nov. Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2195 - 2205. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Nishiyama, H. Yamamoto, T. Uchiumi, and N. Nakashima Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site Nucleic Acids Res., March 12, 2007; 35(5): 1514 - 1521. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Endo and S. Okada Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue. Int J Syst Evol Microbiol, October 1, 2006; 56(Pt 10): 2345 - 2348. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Schulze Phylogeny and genetic diversity of palolo worms (palola, eunicidae) from the tropical north pacific and the Caribbean. Biol. Bull., February 1, 2006; 210(1): 25 - 37. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Silverman and E. T. Kool Quenched autoligation probes allow discrimination of live bacterial species by single nucleotide differences in rRNA Nucleic Acids Res., September 2, 2005; 33(15): 4978 - 4986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Pasquali, H. H. Gan, and T. Schlick Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs Nucleic Acids Res., March 3, 2005; 33(4): 1384 - 1398. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, M. Vancanneyt, I. Cleenwerck, A. M. Lysenko, V. V. Mikhailov, and J. Swings Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1643 - 1648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, M. Vancanneyt, I. Cleenwerck, N. V. Zhukova, M. V. Vysotskii, V. V. Mikhailov, and J. Swings Salegentibacter holothuriorum sp. nov., isolated from the edible holothurian Apostichopus japonicus Int J Syst Evol Microbiol, July 1, 2004; 54(4): 1107 - 1110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, A. M. Lysenko, C. Snauwaert, M. Vancanneyt, J. Swings, M. V. Vysotskii, and V. V. Mikhailov Cellulophaga pacifica sp. nov. Int J Syst Evol Microbiol, March 1, 2004; 54(2): 609 - 613. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Lopez, F. Ruiz-Larrea, L. Cocolin, E. Orr, T. Phister, M. Marshall, J. VanderGheynst, and D. A. Mills Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis Appl. Envir. Microbiol., November 1, 2003; 69(11): 6801 - 6807. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. C. J. Haasnoot, J. F. Bol, and R. C. L. Olsthoorn A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions PNAS, October 28, 2003; 100(22): 12596 - 12600. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, M. V. Vysotskii, and V. V. Mikhailov Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1281 - 1286. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. I. Nedashkovskaya, M. Suzuki, M. V. Vysotskii, and V. V. Mikhailov Arenibacter troitsensis sp. nov., isolated from marine bottom sediment Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1287 - 1290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Itoh, K. Suzuki, P. C. Sanchez, and T. Nakase Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines Int J Syst Evol Microbiol, July 1, 2003; 53(4): 1149 - 1154. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. C. Hoyle and P. G. Higgs Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences Mol. Biol. Evol., January 1, 2003; 20(1): 1 - 9. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-J. Hu Prediction of consensus structural motifs in a family of coregulated RNA sequences Nucleic Acids Res., September 1, 2002; 30(17): 3886 - 3893. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-c. Wang and D. A. Hickey Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes Nucleic Acids Res., June 1, 2002; 30(11): 2501 - 2507. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Schattner Searching for RNA genes using base-composition statistics Nucleic Acids Res., May 1, 2002; 30(9): 2076 - 2082. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Wang and S.-C. Lee Secondary Structure of Mitochondrial 12S rRNA Among Fish and Its Phylogenetic Applications Mol. Biol. Evol., February 1, 2002; 19(2): 138 - 148. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wuyts, Y. Van de Peer, T. Winkelmans, and R. De Wachter The European database on small subunit ribosomal RNA Nucleic Acids Res., January 1, 2002; 30(1): 183 - 185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. E. Olson and A. D. Yoder Using Secondary Structure to Identify Ribosomal Numts: Cautionary Examples from the Human Genome Mol. Biol. Evol., January 1, 2002; 19(1): 93 - 100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wuyts, Y. Van de Peer, and R. De Wachter Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA Nucleic Acids Res., December 15, 2001; 29(24): 5017 - 5028. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Bolivar, J. F. Fahrni, A. Smirnov, and J. Pawlowski SSU rRNA-based Phylogenetic Position of the Genera Amoeba and Chaos (Lobosea, Gymnamoebia): The Origin of Gymnamoebae Revisited Mol. Biol. Evol., December 1, 2001; 18(12): 2306 - 2314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Boucher, H. Huber, S. L'Haridon, K. O. Stetter, and W. F. Doolittle Bacterial Origin for the Isoprenoid Biosynthesis Enzyme HMG-CoA Reductase of the Archaeal Orders Thermoplasmatales and Archaeoglobales Mol. Biol. Evol., July 1, 2001; 18(7): 1378 - 1388. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gorodkin, S. L. Stricklin, and G. D. Stormo Discovering common stem-loop motifs in unaligned RNA sequences Nucleic Acids Res., May 15, 2001; 29(10): 2135 - 2144. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Watanabe, J. Nelson, S. Harayama, and H. Kasai ICB database: the gyrB database for identification and classification of bacteria Nucleic Acids Res., January 1, 2001; 29(1): 344 - 345. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wuyts, P. De Rijk, Y. Van de Peer, G. Pison, P. Rousseeuw, and R. De Wachter Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA Nucleic Acids Res., December 1, 2000; 28(23): 4698 - 4708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. M. Page Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching Nucleic Acids Res., October 15, 2000; 28(20): 3839 - 3845. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||