DPVweb is a

database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

for virologists working on plant viruses combining taxonomic, bioinformatic and

symptom Signs and symptoms are diagnostic indications of an illness, injury, or condition. Signs are objective and externally observable; symptoms are a person's reported subjective experiences. A sign for example may be a higher or lower temperature ...

data.

Description

DPVweb is a central web-based source of information about

virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...

es,

viroid Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants), and most cause diseases, whose respective eco ...

s and satellites of

plants Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars f ...

fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...

and

protozoa Protozoa (: protozoan or protozoon; alternative plural: protozoans) are a polyphyletic group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic debris. Historically ...

. It provides comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. It makes use of a large database that 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. There are currently about 10,000 such sequences. For comparative purposes, DPVweb also contains a representative sequence of all other fully sequenced virus species with an

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

or single-stranded

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

. For each curated sequence the database contains the start and end positions of each feature (

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

, non-translated region, etc.), and these have been checked for accuracy. As far as possible, the nomenclature for genes and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s are standardized within genera and families. Sequences of features (either as DNA or

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for personal computers.

History

The Descriptions of Plant Viruses (DPVs) were first published by the Association of Applied Biologists in 1970 as a series of leaflets, each one written by an expert describing a particular plant virus. In 1998 all of the 354 DPVs published in paper were scanned, and converted into an electronic format in a database and distributed on CDROM. In 2001 the descriptions were made available on the new DPVweb site, providing open access to the now 400+ DPVs (currently 415) as well as taxonomic and sequence data on all plant viruses.

Uses

DPVweb is an aid to researchers in the field of plant virology as well as an educational resource for students of

virology Virology is the Scientific method, scientific study of biological viruses. It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host (biology), ...

and

molecular biology Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

. The site provides a single point of access for all known plant virus genome sequences making it easy to collect these sequences together for further analysis and comparison. Sequence data from the DPVweb database have proved valuable for a number of projects: # survey of

codon Genetic code is a set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome, which links prote ...

usage bias amongst all plant viruses, # two-way comparisons between comprehensive sets of sequences from the families Flexiviridae and

Potyviridae ''Potyviridae'' is a family of positive-strand RNA viruses that encompasses more than 30% of known plant viruses, many of which are of great agricultural significance. The family contains 13 genera that contain 259 species. Structure Potyviri ...

that have helped inform taxonomy and clarify genus and species discrimination criteria, # a survey and verification of the polyprotein cleavage sites within the family Potyviridae.

References

Citation by Danish Institute of Agricultural Sciences

Citation by the John Innes Centre, United Kingdom
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External links

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DPVweb
''EDAM bioinformatics ontology'' {{DEFAULTSORT:Dpvweb Molecular biology Plant taxonomy Biological databases Viral plant pathogens and diseases Virology Ontology (information science) Information science

Description

History

Uses

See also

References

External links