Nucleic Acids Research 2006 34(Database Issue):D382-D385; doi:10.1093/nar/gkj023
Nucleic Acids Research, 2006, Vol. 34, Database issue D382-D385
© The Author 2006. Published by Oxford University Press. All rights reserved
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DPVweb: a comprehensive database of plant and fungal virus genes and genomes
Michael J. Adams* and
John F. Antoniw
Plant-Pathogen Interactions Division, Wheat Pathogenesis Programme, Rothamsted Research Harpenden, Herts AL5 2JQ, UK
*To whom correspondence should be addressed. Tel: +44 1582 763133; Fax: +44 1582 760981; Email: mike.adams{at}bbsrc.ac.uk
Received August 4, 2005. Revised September 21, 2005. Accepted September 21, 2005.
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ABSTRACT
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DPVweb (
http://www.dpvweb.net/) provides a central source of
information about viruses, viroids and satellites of plants,
fungi and protozoa. Comprehensive taxonomic information, including
brief descriptions of each family and genus, and classified
lists of virus sequences are provided. The database also holds
detailed, curated, information for all sequences of viruses,
viroids and satellites of plants, fungi and protozoa that are
complete or that contain at least one complete gene (currently,
n 
9000). For comparative purposes, it also contains a single
representative sequence of all other fully sequenced virus species
with an RNA or single-stranded DNA genome. The start and end
positions of each feature (gene, non-translated region and the
like) have been recorded and checked for accuracy. As far as
possible, nomenclature for genes and proteins are standardized
within genera and families. Sequences of features (either as
DNA or amino acid sequences) can be directly downloaded from
the website in FASTA format. The sequence information can also
be accessed via client software for PC computers (freely downloadable
from the website) that enable users to make an easy selection
of sequences and features of a chosen virus for further analyses.
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INTRODUCTION
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The public sequence databases contain vast amounts of data on
virus genomes but accessing and comparing the data, except for
relatively small sets of related viruses can be very time consuming.
The procedure is made difficult because some of the sequences
on these databases are incorrectly named, poorly annotated or
redundant. The NCBI Reference Sequence project (
1) provides
a comprehensive, integrated, non-redundant set of sequences,
including genomic DNA, transcript (RNA) and protein products,
for major research organisms. This now includes curated information
for a single sequence of each fully sequenced virus species.
While this is a welcome development, it can only deal with complete
sequences. DPVweb aims to provide a comprehensive source of
high quality sequence and taxonomic information for all fully
sequenced genes of viruses, viroids and satellites of plants,
fungi and protozoa. An important feature is the opportunity
to access genes (and other features) of multiple sequences quickly
and accurately. Thus, for example, it is easy to obtain the
nucleotide or amino acid sequences of all the available accessions
of the coat protein gene of a given virus species or for a group
of viruses. To increase its usefulness further, DPVweb also
contains a single representative sequence of all other fully
sequenced virus species with an RNA or single-stranded DNA (ssDNA)
genome.
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ORIGIN OF THE PROJECT
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The project developed as an electronic version of the Association
of Applied Biologists (AAB) descriptions of plant viruses (DPV)
(
2). This is a standalone program for PCs (first released in
1998) that includes detailed descriptions of selected plant
viruses together with information on taxonomy and sequences.
It provides a comprehensive resource that is widely used for
teaching, disease management and research. As part of this program,
software (DPVMap) was written to display selected virus sequences
interactively. A separate enhanced feature table (EFT) file
written for each sequence contains the start and end nucleotide
positions of the features [e.g. open reading frames (ORFs) and
untranslated regions] within the sequence. In DPVMap any of
the features of the sequence can be dragged into a sequence
editor to display its nucleotide sequence (as RNA or DNA), or
the predicted amino acid sequence of an ORF. Annotations provide
for the correct display of reverse complementary sequences and
of those incorporating a frameshift or intron. Sequence features
are checked for accuracy and, as far as possible, nomenclature
for genes and proteins are standardized within genera and families
to make it easier to compare features from different viruses.
Additional information (e.g. polyprotein cleavage sites) may
also be added by comparison with related sequences. From a modest
beginning, this has expanded to become a comprehensive resource
(see Current Coverage section, below). The information contained
in the individual EFT files is valuable because it has been
checked for accuracy and is often more detailed than that provided
in the original sequence file from EMBL/Genbank/DDBJ. However,
the EFT files can only be used with DPVMap and to examine one
sequence at a time. We therefore decided to transfer this information
together with the sequences themselves into a database table
so that multiple datasets could be selected and extracted easily
and then used for further analysis. Although the standalone
program is still available in CD-ROM format, much of the information,
including that of the sequence features, is now also provided
through the website described here.
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DESCRIPTION OF THE WEBSITE
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The home page of DPVweb (
http://www.dpvweb.net/) provides simple
and user-friendly access to all the features of the site. There
are five major sections to the site, accessed from a menu bar
at the top of the page.
Home
This provides an overview of the site and an introduction to plant viruses in general.
DPV
This section contains the detailed descriptions of individual viruses. Over 400 viruses or virus groups are included. Numbers 1–354 were originally published in paper form by the AAB between 1970 and 1989, while additional descriptions have been added since 1998. A small editorial team of internationally renowned virologists commission and edit the descriptions, which are written by specialists. The descriptions provide comprehensive information on virus diseases, geographical distribution, host range, symptoms, transmission, vectors, serology, relationships with other viruses, purification protocols, properties of virus particles, particle structure and composition, molecular structure, genome properties, cytopathology, ecology and control procedures as well as references to the scientific literature. The descriptions also include images of symptoms, electron micrographs of virus particles, genome maps and so on. A menu item allows a search to be made using a text query on the complete set of descriptions, and this can be limited to selected fields (subheadings in the descriptions) if required.
Notes
The notes are a brief description of each family and genus included within the project (i.e. all viruses except those with a double-stranded DNA (dsDNA) genome; see Current Coverage section, below). This includes (i) a description of particle morphology and genome organization (where known); (ii) a genome map (usually of the genus type member); (iii) a representative electron micrograph (for plant viruses only); (iv) a list of species with their acronyms and synonyms for each genus with links to the plant virus descriptions; (v) a list of accession numbers (and links to the sequences) used by EMBL/Genbank/DDBJ databases for all the sequences in the family or genus together with the description from the sequence header (for viruses, satellites and viroids infecting plants, fungi and protozoa only); and (vi) a list of ‘curated sequences’ for each virus, providing links to access the sequences of individual genes or other features (see Access to Sequence Features section, below). A menu item allows a search to be made amongst all the virus (and strain/synonym) names in the database. This returns a list of all matching names, with links to the appropriate genus notes page and, where appropriate, to the specialist description.
Sequences
This provides lists of the accession numbers used by EMBL/Genbank/DDBJ databases for all the sequences of viruses, satellites and viroids infecting plants, fungi and protozoa. These have been checked to ensure that, as far as possible, they are allocated to their correct species. Each accession number is linked so that the sequence can be fetched from EMBL.
Analysis
This provides links to client software that accesses the data from the user's PC (see Client Software section, below).
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TECHNICAL DETAILS
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All data are stored in a MySQL database on an Apache web server
and accessed using PHP scripts to display the data on the web
page and to generate XML output for the web-enabled client software.
Regular searches are made at EMBL for virus sequences that are
new or that have been updated. EFT files are created for the
standalone DPV program as described above (Origin of the Project
section) and used to test the accuracy of the data. The information
is transferred into XML database files for use by the standalone
DPV program, and the public web database is then updated once
a month.
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CURRENT COVERAGE
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The notes and taxonomic information cover all RNA and ssDNA
viruses, including the reverse-transcribing viruses and related
retroelements and therefore includes all viruses except those
with a dsDNA genome. The sequence database holds detailed information
for all sequences of viruses, viroids and satellites of plants,
fungi and protozoa that are complete or that contain at least
one complete gene (currently,
n 9000). For comparative purposes,
it also contains a single representative sequence of all other
fully sequenced virus species within the taxa covered (
750 sequences).
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ACCESS TO SEQUENCE FEATURES
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Curated sequences are listed under the current species name
from the appropriate genus notes page. The descriptions are
shorter, but usually more informative than those in the complete
sequence lists. The accession number is linked to the entire
sequence file. Next to each accession number is a check box
for selection of one or more sequences within the genus. At
the top and bottom of each page is a ‘Get Features of
Selected Sequences’ button and when selected, a sorted,
collated list of all the features within the sequences is displayed.
These features can be selected using the check boxes and the
type of FASTA output (DNA or protein) selected from the radio
button at the bottom of the page. Finally the ‘Get Fastas
of Features’ button at the bottom of the page will provide
the sequences in a form that can be copied and pasted into further
applications or saved to file. The process is illustrated for
the coat proteins of members of the genus
Bromovirus in
Figure 1.
The usefulness of the database lies in the ability to select
multiple sequences of a species or genus and to obtain the sequences
of one or more genes very rapidly. For example, in a recent
test, a single complete sequence was selected from each species
in the genus
Begomovirus. From this point, the amino acid sequences
of the coat proteins of each of the (139) species were obtained
in
70 s.
View larger version (57K):
[in this window]
[in a new window]
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Figure 1 Sequence of screen shots from DPVweb.net showing (left) selection of curated sequences from species in the genus Bromovirus, (centre) selection of Coat protein feature and protein output and (right) the FASTA output of the coat protein genes.
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CLIENT SOFTWARE
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As an additional method for accessing and analysing the sequence
data, some client software has been written in Delphi that can
be freely downloaded from the website to the user's PC. Three
programs are currently available that use a similar interface
to select the virus species, accession number(s) and sequence
feature(s). Depending on the software, the program will then
either (i) download the FASTA sequences (DNA or protein); (ii)
calculate codon usage statistics; or (iii) predict transmembrane
domains in the protein sequence using TMpred (
3). Requests for
data are made using http to the server and data is returned
in XML format. While all of the data are centralized on the
web database to make it easier to update, for speed of analysis
and to reduce the server load, the subsequent calculations are
handled by the client software on the PC and not by the PHP
scripts. The client application makes http requests to the web
server for information selected by the user and parses the XML
data returned and formats it for display or processes it as
required.
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EXAMPLES OF USE
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Sequence data from the database have proved valuable for a number
of projects: (i) survey of codon usage bias amongst all plant
viruses (
4), (ii) two-way comparisons between comprehensive
sets of sequences from the families
Flexiviridae and
Potyviridae that have helped inform taxonomy and clarify genus and species
discrimination criteria (
5,
6), (iii) a survey and verification
of the polyprotein cleavage sites within the family
Potyviridae (
7) together with dedicated web pages at
http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.
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CONCLUSIONS AND FUTURE PLANS
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DPVweb and its associated tools provide an accurate, comprehensive
and powerful resource for analysis of plant virus sequences.
We plan to improve annotation of genes and proteins to provide
more functional information where this is available. We are
also seeking collaborative opportunities to extend the usefulness
of this project.
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ACKNOWLEDGEMENTS
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We thank our colleagues in the DPV project (Drs Hugh Barker,
Tony Murant, Teifion Jones and David Robinson at Scottish Crop
Research Institute and Phil Jones at Rothamsted Research) for
their encouragement and suggestions. We thank the AAB for their
support, in particular by funding the development of the standalone
DPV program and for sponsoring the DPVweb internet site. Rothamsted
Research receives grant-aided support from the Biotechnology
and Biological Sciences Research Council of the United Kingdom.
Funding to pay the Open Access publication charges for this
article was provided by Rothamsted Research Limited (
http://www.rothamsted.ac.uk/).
Conflict of interest statement. None declared.
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REFERENCES
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- Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Helmberg, W., et al. (2005) Database resources of the National Center for Biotechnology Information Nucleic Acids Res, . 33, D39–D45[Abstract/Free Full Text]
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- Adams, M.J., Antoniw, J.F., Barker, H., Jones, A.T., Murant, A.F., Robinson, D. Descriptions of Plant Viruses on CD-ROM, (1998) Wellesbourne, Warwick, UK Association of Applied Biologists
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- Hofmann, K. and Stoffel, W. (1993) TMbase—a database of membrane spanning proteins segments Biol. Chem. Hoppe-Seyler, 374, 166
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- Adams, M.J. and Antoniw, J.F. (2004) Codon usage bias amongst plant viruses Arch. Virol, . 149, 113–135[Medline]
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- Adams, M.J., Antoniw, J.F., Bar-Joseph, M., Brunt, A.A., Candresse, T., Foster, G.D., Martelli, G.P., Milne, R.G., Zavriev, S.K., Fauquet, C.M. (2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation Arch. Virol, . 149, 1045–1060[Medline]
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- Adams, M.J., Antoniw, J.F., Fauquet, C.M. (2005) Molecular criteria for genus and species discrimination within the family Potyviridae Arch. Virol, . 150, 459–479[CrossRef][Medline]
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- Adams, M.J., Antoniw, J.F., Beaudoin, F. (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae Mol. Plant Pathol, . 6, 471–487[CrossRef]
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