Virus databases
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[edit] Categories which link here
[edit] Virus databases - Quick Links
[edit] Virus databases - Web Resources
Viral Bioinformatics Canada: VBRC-University of Victoria is an online resource providing access to curated viral genomes and a variety of tools for comparative genomic analyses. The resource includes tools such asVOCs
, JDotter, Base-by-Base, VGO, GraphDNA, JIPS, ReHAB , Hydrophobicity Grapher etc. At the core of the system is VOCs (Viral Orthologous Clusters), a viral genomic database with built-in tools that allow users to retrieve, display and analyze the genes, ortholog groups and genomes within the database. This curated database (containing Adeno-, Arena-, Asfar-, Baculo-, Bunya-, Corona-, Filo-, Flavi-, Herpes-, Irido-, Paramyxo-, Pox- and Togaviridae) is the source of information for other programs of the workbench used for whole genome alignments, genome display or gene/protein sequence analysis. Many of these tools can also be used with manually-inputted sequence data. The workbench tools are Java-based to allow all users, regardless of computer skill-level, to access and analyze the data.
ViTa prediction of host microRNAs targets on viruses. Using known miRNAs from miRBase, virus data are collected and referred from ICTVdB, VBRC and VirGen, and validated miRNA targets on viruses derived from the literature, miRanda and TargetScan were utilized to predict miRNA targets within virus genomes.
[edit] Influenza Databases
Influenza Virus Database (IVDB) is an integrated information resource and analysis platform for genetic, genomic, and phylogenetic studies, which aims to be a central database specialized in influenza viruses (IVs). Hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) displays worldwide geographic distribution of given viral genotypes, coupling genomic data with epidemiological data. Features BLAST, multiple sequence alignment and phylogenetic analysis tools as well as pre-computed alignments and polymorphisms of IV genes and proteins, results as SNP distribution plots and minor allele distributions.
[edit] HIV Databases
HIV Databases HIV Databases The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. The website also gives access to a large number of analysis tools.
The HIV positive selection mutation database provides detailed selection pressure maps of HIV protease and reverse transcriptase, which are molecular targets of antiretroviral therapy. Includes a very large HIV sequence dataset (from 50,000 clinical samples, generously contributed by Specialty Laboratories, Inc.), which facilitated high-resolution selection pressure mapping on individual sites as well as how selection pressure at one site is affected by mutations on other sites. Includes datasets from public databases. Comparison between datasets enables cross-validation with independent datasets and also specific evaluation of the effect of drug treatment.
[edit] Hepatitis Databases (HCV, HBV)
euHCVdb: the European hepatitis C virus database is a collection of computer-annotated sequences based on reference genomes, mainly dedicated to HCV protein sequences, 3D structures and functional analyses. Facilitates the research into the genetic and structural variability of all available HCV sequences, for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development.
HepSEQ is a web-based library of public health and molecular data relating to hepatitis B virus (HBV) hosted by HPA, UK. Useful for surveillance, HBV case management and for research. Facilitiates deposition, search and manipulation of data to create reports on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection. Facilitates analysis of data about HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against deposited strains.
