Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Jan 1;32(Database issue):D101-3.
doi: 10.1093/nar/gkh065.

The European ribosomal RNA database

Jan Wuyts  1 , Guy Perrière, Yves Van De Peer
Affiliations

The European ribosomal RNA database

Jan Wuyts et al. Nucleic Acids Res. .

Abstract

The European ribosomal RNA database aims to compile all complete or nearly complete ribosomal RNA sequences from both the small (SSU) and large (LSU) ribosomal subunits. All sequences are available in aligned format. Sequence alignment is based on the secondary structure of the molecules, as determined by comparative sequence analysis. Additional information about the sequences, such as taxonomic classification of the organism from which they have been obtained, and literature references are also provided. In order to identify the closest relatives to newly determined sequences, BLAST searches can be performed, after which the best matching sequences are aligned and a phylogenetic tree is inferred. As of 2003, the European ribosomal RNA database is maintained at Ghent University (Belgium). The database can be consulted at http://www.psb.ugent.be/rRNA/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Example of the newly implemented tool to compare newly determined sequences with other sequences available in the rRNA databases. In this case, the LSU rRNA sequence of Arabidopsis thaliana (EMBL acc. no. AC006837) was BLAST-ed to the complete LSU rRNA database. Next, the 24 best scoring sequences were selected and an alignment was constructed and displayed in the Jalview applet (back). From this alignment, a neighbor-joining tree (11) was constructed and displayed by the use of the ATV applet [front (12)].
See this image and copyright information in PMC

References

    1. Wimberly B.T., Brodersen,D.E., Clemons,W.M.,Jr, Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327–339. - PubMed
    1. Ban N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science, 289, 905–920. - PubMed
    1. Wuyts J., Van de Peer,Y. and De Wachter,R. (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res., 29, 5017–5028. - PMC - PubMed
    1. Hancock J.M. and Dover,G.A. (1990) ‘Compensatory slippage’ in the evolution of ribosomal RNA genes. Nucleic Acids Res., 18, 5949–5954. - PMC - PubMed
    1. Stoesser G., Baker,W., van den Broek,A., Garcia-Pastor,M., Kanz,C., Kulikova,T., Leinonen,R., Lin,Q., Lombard,V., Lopez,R. et al. (2003) The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res., 31, 17–22. - PMC - PubMed

Publication types