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{at}rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide
Web (WWW) (http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers
provide ribosomal probe checking, screening for possible chimeric rRNA
sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.
The Ribosomal Database Project (RDP) provides data, programs and services
related to the ribosome. In this paper we summarize these offerings, the
changes that have been introduced since last year's description (
1
) and some future features.
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. They are organized and presented in an
aligned and phylogenetically ordered form. Each sequence is annotated with its
organismal source (for cultured organisms: the genus, species, culture
collection numbers, etc.), cellular compartment, origin of sequence data
(usually a literature citation) and other relevant information. If multiple
versions of a given sequence exist, the RDP attempts to select by a variety of
criteria (which include the frequency of putative sequence errors and
completeness) only one of the versions for release. As a consequence, the
number of released sequences is lower than the number of existing sequences.
The RDP staff also examines the original publications and updates annotations,
strain designations and organism names. Submitters and/or the public sequence
databases are notified of possible errors.
The small subunit (SSU) rRNA alignments currently comprise sequences from ~140 Archaea, 2700 Bacteria (including chloroplasts and a few plant
mitochondria) and 440 Eucarya (an alignment supplied by M. L. Sogin, Woods Hole
Marine Biology Laboratory, MA). A representative alignment of 98 prokaryotic
small subunit rRNA sequences is also available. The number of large subunit
(LSU) rRNA sequences remains at 150.
A phylogenetic tree is available for the sequences in the posted prokaryotic and
eukaryotic (new this year) SSU rRNA alignments. They have been assembled from
appropriately overlapping subtrees, each of which has been inferred using
maximum-likelihood analysis (
4
,
5
). The current trees (and subsets of them) are available in printable text,
PostScript and Newick formats. The RDP also offers a collection of SSU and LSU
rRNA secondary structure diagrams in PostScript format generated and supplied
by R. Gutell
et al.
(
6
). Also new this year is the corresponding taxonomic listing for SSU eukaryotic
rRNA sequences.
As stated in last year's article, the RDP has made available this year unaligned
data sets for use with the SIMILARITY_RANK, CHECK_PROBE and CHECK_CHIMERA
commands (see description of these commands in Table
1
). The current release contains 5500 and 1400 sequences respectively for the SSU
and LSU data sets.
To facilitate access to specific rRNA aligned and unaligned sequences, the RDP
offers subdirectories containing GenBank-formatted files of each sequence (directory names: aligned/sequences/[A-Z] and unaligned/sequences/[A-Z]).
During the past year, an RDP WWW server has been developed. The initial part of
its Home Page is shown in Figure
1
.
Table 2
Research assisted by any RDP service should cite: the Ribosomal Database Project
(RDP) at the University of Illinois in Urbana, IL; the release number and this
article (i.e. Maidak
et al
., 1996). Please state which data, programs and services were used and the
method of access.
The RDP data and analysis services can be found at URL:
http://rdpwww.life.uiuc.edu/.
The RDP data can be accessed via anonymous ftp to rdp.life.uiuc.edu. Once you
are logged in (using a user-id of `anonymous' and your electronic mail address for password), examine
the 00README files, which describe the organization of the data and programs.
The address of the automated electronic mail server is server@rdp.life.uiuc.edu.
To obtain an overview of what data and services are currently available, send a
mail message with the phrase `help' as the body of the message. (Full command
descriptions can be obtained by sending `help complete'). If your electronic
mail address is unknown to the e-mail server, you will also receive a registration form. After returning
the completed registration form, you will be automatically notified when new
data or services become available.
The RDP gopher host name is rdpgopher.life.uiuc.edu. Gopher access to RDP data
through the WWW is also available (URL: gopher://rdpgopher.life.uiuc.edu/).
Electronic mail correspondence with RDP staff should be addressed to
rdp{at}phylo.life.uiuc.edu. Those without access to electronic mail may contact
the RDP curator (B.L.M.) via telephone (+1 217 333 5866), FAX (+1 217 244 6697)
or regular mail.
Future plans for the RDP include improvements (i) in the display of and
interaction with the phylogenetic trees, (ii) in the presentation and output
options of the SUGGEST_TREE command and (iii) an improved version of the
CHECK_PROBE function. Also planned is a sequence evaluation program, which
assesses the quality of a user-supplied sequence, reporting back possible sequencing errors and/or
idiosyncrasies, as well as a `sequence signature' which defines the approximate
taxonomic position of the sequence.
We thank R. Gutell (and his colleagues) and M. L. Sogin for providing their data
collections. The RDP is largely supported by the National Science Foundation,
Biological Instrumentation and Resources Division.
Convert_aln
A sequence alignment format conversion program for UNIX and VAX/VMS systems.
DNArates
A maximum likelihood method to estimate site-specific rates of nucleotide substitution from a sequence alignment and a
user-defined phylogenetic tree. Data formats are similar to those used in J.
Felsenstein's PHYLIP package. Compatible with a wide variety of computers.
Editor_AE2
An alignment editor and analysis program written by T. Macke for UNIX systems.
Editor_GDE
The Genetic Data Environment sequence alignment editing and analysis package
written by S. Smith. Posted version is for Sun Microsystems computers.
EPSFilter
Macintosh program for working with Encapsulated PostScript (EPS) files written
by B. Fowler.
fastDNAml
A maximum likelihood tree inference program based on version 3.3 of J.
Felsenstein's DNAML. It has features to facilitate analysis of a larger number
of taxa. Compatible with a wide variety of computers.
GraphicConverter
Macintosh program for conversion between graphics formats written by T. Lemke.
Readseq
A suite of sequence format conversion programs written by D. Gilbert. Compatible
with a wide variety of computers.
SeqEdit
An alignment editor and analysis program for VAX/VMS systems.
Subalign
A program to extract specified rows and columns from an alignment. For UNIX and
VAX/VMS systems.
TreeTool
A X-windows-based phylogenetic tree manipulation program for Sun Microsystems
computers
REFERENCES
Return