Nucleic Acids Research Advance Access originally published online on November 6, 2006
Nucleic Acids Research 2007 35(Database issue):D141-D144; doi:10.1093/nar/gkl815
Nucleic Acids Research, 2007, Vol. 35, Database issue D141-D144
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dbRES: a web-oriented database for annotated RNA editing sites
Tao He,
Pufeng Du and
Yanda Li*
Bioinformatics Division, TNLIST and Department of Automation Tsinghua University, Beijing 100084, China
*To whom correspondence should be addressed: Tel: +86 10 62794295; Fax: +86 10 62794295; Email: daulyd{at}tsinghua.edu.cn
Received August 7, 2006. Revised October 3, 2006. Accepted October 4, 2006.
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ABSTRACT
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Although a large amount of experimentally derived information
about RNA editing sites currently exists, this information has
remained scattered in a variety of sources and in diverse data
formats. Availability of standard collections for high-quality
experimental data will be by of great help for systematic studying
of RNA editing, especially for developing computational algorithm
to predict RNA editing site. dbRES (
http://bioinfo.au.tsinghua.edu.cn/dbRES)
is a public database of known RNA editing sites. All sites are
manually curated from literature and GenBank annotations. dbRES
version 1.1 contains 5437 RNA editing sites of 251 transcripts,
covering 96 organisms across plant, metazoan, protozoa, fungi
and virus. dbRES provides comprehensive annotations and data
summaries, including (but not limited to) transcript sequences,
RNA editing types, editing site locations, amino acid changes,
organisms, subcellular organelles (if available), cited references,
etc. A user-friendly web interface is developed to facilitate
both retrieving data and online display of RNA edit site information.
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INTRODUCTION
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RNA editing refers to post-transcriptional modifications of
RNA molecules, and represents a class of mechanisms that contribute
to the complexity of the transcriptome (
1). RNA editing occurs
in the nucleus, as well as in mitochondria and plastids (
2).
To date, these modifications have been observed in plants, animals,
fungi and virus (
2–
6). The diversity of this widespread
phenomenon includes nucleotide modifications, nucleotide deletions
and insertions, either in coding or non-coding region of RNA,
which can occur concomitantly with transcription and splicing
processes (
2–
4,
7,
8).
Two public databases, EdRNA (http://edrna.mbc.nctu.edu.tw140.113.239.182/%7Emot/index.php) and Editing Sites Database (9), store putative RNA editing sites that have been predicted using computational methods. While these resources have greatly contributed to the study of RNA editing, the ever-increasing availability of experimental RNA editing data remains scattered under a variety of diverse formats and sources. Availability of standard collected high-quality data is important to design novel computational approaches for identifying RNA editing sites on transcripts. We present dbRES, a collection of experimentally verified RNA editing-sites. dbRES is manually curated from primary literature and annotations in GenBank. To our knowledge, dbRES is the first database containing kinds of up-to-date experimentally reported RNA editing sites.
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DATABASE CONSTRUCTION
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Data collection in dbRES is based on a three-step strategy.
First, the latest version of GenBank (Release 154) (
10) is downloaded
as the data sources, and entries containing the keyword ‘RNA
editing’ are obtained as subset 1. Second, the GenBank
accession numbers of the edited transcripts in each bibliographical
reference are used to retrieve the sequences from GenBank data
sources as subset 2. Finally, for some RNA editing sites with
only direct support in the literature, the details are manually
curated as subset 3. Once this data has been collected, subsets
1, 2 and 3 (including sites, sequences and annotations) are
manually curated to ensure consistency of the data and eliminate
redundancy.
Data storage of dbRES is based on MySQL database system. All the data, including editing sites, annotations and sequences, are integrated in a single complex-table with several external links to text files. Because data accumulates continually, data archiving in dbRES is an on-going process that includes automatic, periodic updates to the central MySQL database.
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DATABASE CONTENTS
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dbRES currently contains 5437 RNA editing events for 251 transcripts
covering 96 organisms, including plants, metazoa, protozoa,
fungi and virus. Every RNA editing event is categorized as one
of 16 different types (e.g. C to U, U to C, A to I).
Table 1 shows the distribution of data from dbRES across these different
categories of edits and distribution of data across different
species is given in Supplementary Table 1.
Neighboring nucleotide preferences for edits of the three main
types (C to U, U to C and A to I) are systematically analyzed
based on the nucleotide frequency at positions –2, –1,
0, 1 and 2 relative to each editing site. This analysis employs
statistical methods that are standard for the RNA editing field
(
11–
13).
Figure 1 presents results of this analysis (for
the contents of dbRES version 1.1) in the form of sequence logos.
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WEB INTERFACE
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Data browser
The dbRES database is freely available at
http://bioinfo.au.tsinghua.edu.cn/dbRES.
The browser function of the dbRES web site supports browsing
by species and browsing by editing type. The browser organizes
information about species according to a NCBI taxonomy tree
(
10,
14). Users can expand the tree level-by-level. At the deepest
level, gene names corresponding to the species are shown as
links to the database viewer (described in the next section).
The upper part of
Figure 2 shows an example of these browsing
functions.
Data viewers
The dbRES web site allows several options for viewing data.
One useful viewing mode is by individual RNA editing site. While
viewing data for individual sites, information about the corresponding
gene is displayed, including related information from GenBank,
and links to related external pages (e.g. the associated GenBank
page, or MiRBase in the case of MicroRNAs). Information about
the original sequence, organism and subcellular organelle (where
appropriate) is also displayed. For RNA editing events that
have been reported in a PubMed-indexed publication, links to
the PubMed abstract are provided. Another useful viewing mode
is by transcripts, and in this mode each associated editing
event is indicated along with links to display those individual
events. The translated amino acid sequences of the edited and
their genomic sequences can be viewed when the editing site
locates in CDS region. Examples of these data viewing functions
can be found in
Figure 2.
Search engine
Several options are provided for searching dbRES. The web-interface for the dbRES search engine is displayed in Figure 3. The searching functions of dbRES allow users to retrieve data by querying three fields: gene name, organism and RNA editing type. This search function assists users to retrieve only the data in which they are interested. dbRES can also be searched by using a querying sequence. This function is implemented by running the BLAST program (15) on the dbRES server, with the result automatically parsed to generate a list of dbRES accession numbers. The protocol and the interface for the sequence query function are also shown in Figure 3.
Database download and mirror service
For the convenience of users, we provide dbRES for downloading
in two formats: an annotated flat text package and an SQL script
package. In addition to these packages, dbRES is also provided
the form of a free mirror-service. The mirror-service package
contains all web site elements and a set of data processing
programs (as PHP scripts) with detailed instructions for setting
up the mirror site.
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CONCLUSIONS AND FUTURE WORK
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The dbRES database has been developed to fill an existing gap
in the availability of consistent and high-quality data collection
to use in training and evaluating computational methods for
discovering RNA editing sites. The collection described here
contains 5437 experimental RNA editing sites identified in plants,
animals, fungi and virus. In the next release, we plan to increase
the number of A to I editing sites and other types of newly
reported editing sites.
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SUPPLEMENTARY DATA
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Supplementary Data are available at NAR Online.
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ACKNOWLEDGEMENTS
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We thank Fei Li and Jin Gu for his critical reading and suggestion
of the manuscript. We thank Andrew Smith and Allison Blum for
their kind help to carefully copy-edit the manuscript. This
work is supported partially by The National Basic Research Program
(2004CB518605) and National Science Foundation of China (60405001
and 60572086). Funding to pay the Open Access publication charges
for this article was provided by National Science Foundation
of China.
Conflict of interest statement. None declared.
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Footnotes
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The authors wish it to be known that, in their opinion, the
first two authors should be regarded as joint First Authors
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