ABSTRACT
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The
offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA)
sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and
various software for handling, analyzing and displaying alignments and trees.
The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail
(server@rdp.life.uiuc.edu), gopher (rdpgopher.life. uiuc.edu) and WWW
(http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide
ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences,
automated alignment, and a suggested placement of an unknown sequence on an
existing phylogenetic tree.
The Ribosomal Database Project (RDP) provides data, programs and services
related to the ribosome. This paper describes changes that have been introduced
since last year's description (
1
). Details about currently available analysis functions, data, and available
programs can be found on the servers described below.
The ribosomal RNA sequences in the RDP alignments are drawn from major sequence
repositories [GenBank (
2
) and EBI (
3
)] and direct submissions to the RDP. During the past year, RDP staff extended
extensive effort to obtaining and examining all publications related to the
sequencing of small subunit ribosomal RNA. Bibliographic citations from the
sequence databases were updated from `Unpublished' when possible and corrected
when found to be in error. In each instance it was confirmed that (i) the
published paper referred to the given public database sequence and (ii) the
feature annotations were consistent with the published paper.
More than 800 small subunit (SSU) rRNA sequences have been added to the
prokaryotic alignment, bringing the total to over 3600. The eukaryotic
alignment has been extensively reworked, and several hundred new sequences
added as well. New this year is an alignment of ~1000 small subunit mitochondrial sequences. The full molecular length
ranges from 611 bp for
Trypanosoma brucei
to 2023 bp for
Lupinus luteus
representing a tremendous amount of variation among organisms.
Phylogenetic trees are available for the sequences in the posted prokaryotic,
eukaryotic and mitochondrial SSU rRNA alignments. They have been built by
sequential addition of sequences to starting trees of full-length sequences, all using a maximum-likelihood criterion (
4
,
5
). The RDP also offers a collection of SSU and LSU rRNA secondary structure
diagrams in PostScript format generated and supplied by R. Gutell and his
collaborators.
To facilitate access to specific rRNA aligned and unaligned sequences, the RDP
offers subdirectories containing GenBank-formatted files of each sequence (directory names: alignments/sequences/[A-Z] and unaligned/sequences/[A-Z]).
All of the RDP data and analysis services can be accessed through the RDP World
Wide Web server: http://rdpwww.life.uiuc.edu/ . The Web pages have been
extensively revised. Figure
1
depicts the current Home Page. Links to related sites have also been expanded.
Research assisted by any RDP service should cite: the Ribosomal Database Project
(RDP) at the University of Illinois in Urbana, Illinois; the release number;
and this article (i.e., Maidak
et al
., 1997). Please state which data, programs and services were used and the
method of access.
We thank R. Gutell (and his colleagues) and M. L. Sogin for providing their data
collections. The RDP is largely and currently supported by the National Science
Foundation, Biological Instrumentation and Resources Division.
REFERENCES
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