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DenVirDB

DENvirDB is the sequence repository of Dengue virus that includes the whole genome sequences reported in endemic areas such as India, Bangladesh, Sri Lanka, East Timor, Philippines, Malaysia, Papua New Guinea, Brunei and China. It provides comprehensive information of complete genome sequences of Dengue virus isolates of Asian countries which are collected from NCBI and stored in manually designed file. DENvirDB has been developed with two data tables, one consists of complete genome database for four serotypes such as DENV1, DENV 2, DENV3, DENV4, and another table comprises of protein annotation details of each protein sequences. The protein annotation includes sequences of structural and nonstructural proteins. It is developed with the objective of providing the genomes sequences and its protein sequences in one platform. The special feature of DenVirDB is that it gives the comprehensive information on the physico-chemical and structural properties of both structural and non-structural proteins. Each genome of DENV contains ten entries of protein sequences that includes three structural and seven non-structural proteins.The important fields such as molecular weight, pI, amino acid composition, hydropathy plot, Topology prediction, Domain details, secondary structure prediction has been incorporated in each protein entries. The sequences can be retrieved in FASTA format.

Database architecture

Genome database

The information of each sequence are given in file format (entry) which contains three sections. The first part of the file tells about the sequence information such as name, accession number, genome size, and organism. For our convenience, the accession number is given based on serotypes and type of sequences.It includes serotypes.sequences type followed by five digit number(DEN(1/2/3/4).(G/P)00000) for example genome sequences are represented as DEN3.G00001 and for protein sequences DEN3.P00001. The second part of the file includes the sequence and genome coordinates of structural and nonstructural proteins. The name of each protein sequences is hyperlinked to obtain the annotated result of the protein. The third part of the file contains the references. Totally, it has 98 complete genome sequences of four serotypes reported in nine countries


Protein database

It contains 1920 proteins of structural and nonstructural protein (Capsid, prM, envelope protein, NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5) of four serotypes of dengue virus in nine countries.The protein entry file contains three sections such as general information,physico-chemical properties and structual information that provide the comprehensive information about each protein sequences. General information includes the protein name, organism name, taxonomic lineage and accession number. The second section contains Physicochemical properties such as molecular weight, pI, amino acid composition, hydropathy plot. The structual details such as protein topology, domain, secondary structure and links to PDB are given in the last section. Each entries are end with the protein sequences and references.

Database Search

Database can be searched for either viral genomes or proteins based on countries and serotypes in basic search. Complete genome search provides the list of entries available based on the selection criteria.which can be further accessed to retrieve the feature table and the secquences of a particular genome . Similarly protein search also facilitates countries and serotypes based search along with specific viral protein.

Classification

Group: Group IV
Family: Flaviviridae
Genus: Flavivirus
Species: Dengue virus









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