The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy - PubMed (original) (raw)

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

J R Cole et al. Nucleic Acids Res. 2003.

Abstract

The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

PubMed Disclaimer

Similar articles

Cited by

References

    1. Maidak B.L., Cole,J.R., Lilburn,T.G., Parker,C.T., Saxman,P.R., Farris,R.J., Garrity,G.M., Olsen,G.J., Schmidt,T.M. and Tiedje,J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res., 29, 173–174. - PMC - PubMed
    1. Bruno W.J., Socci,N.D. and Halpern,A.L. (2000) Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol., 17, 189–197. - PubMed
    1. Brown M.P.S. (2000) Small subunit ribosomal RNA modeling using stochastic context-free grammar. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). San Diego, California, USA, pp. 57–66. - PubMed
    1. Garrity G.M., Winters,M., Kuo,A.W. and Searles,D.B. (2002) Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, 2nd Edn, Springer-Verlag, NY.
    1. Wheeler D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Database Resources of the National Center for Biotechnology Information. Nucleic Acids Res., 28, 10–14. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources