This table of links is interactive: keyword search can be performed in the search box and combined.
For example "HBV" will list the links relevant to this virus, or "HIV drug" the sites related to the drugs against HIV.
| Sites | Comment | Interface | Specificity |
|---|---|---|---|
| dsRNA viruses resource | various information about taxonomy, outbreaks and sequences of dsRNA viruses | web(last update 2009) | Reoviridae, Cystoviridae, Birnaviridae, Totiviridae |
| Reference Center for bacterial viruses | Collects, conserves and distributes reference phages and information. | web | phages |
| ACLAME | database dedicated to the collection and classification of mobile genetic elements (MGEs) | web | phages |
| Bioafrica.net | research, software and publications based on HIV, HCV and few other viruses | web | HIV, HCV, HPV |
| UCSC Ebola Genome Portal | Collection on data on the 2014 ebola outbreak | web | Ebolavirus |
| BROAD institute Dengue virus database | Dengue virus sequences and analysis tools | web | Dengue |
| Virology blog | Blog focussed on virus molecular biology | web | All viruses |
| NetPicoRNA | Prediction of picornaviridae cleavage sites on amino acid sequences | web | Picornaviridae |
| NetCorona | Prediction of Coronavirus 3CL Proteinase cleavage sites on amino acid sequences | web | Coronaviridae |
| VirusWorld | Virus capsids pictures and movies | web | All viruses |
| Retroviruses | Detailed knowledge on Retrovirus molecular biology | Online book | Retroviridae, HIV |
| INTRINSIC STRUCTURE OF VIRUS CAPSIDS | Details on capsid structure and nomenclature | Online book | all viruses |
| Iterative Virus Assembler (IVA) | tool to assemble virus genomes from NGS/metagenomics | download | metagenome |
| Baculovirus molecular biology | Detailled knowledge on baculovirus molecular biology | Online book | Baculovirus |
| Virology.ca | Databases and resources for viral genomics | web | Asfarviridae, Herpesviridae, Poxviridae, Iridoviridae, Baculoviridae |
| UniProt | protein sequences of all public viral ORF | web | All viruses |
| RNA virus database | Sequence analysis tools and data for RNA viruses | web | RNA viruses |
| HIV-1 databases | sequence, vaccine, drug resistance and immunology databases | web | HIV-1 |
| IRESite | database of experimentally verified IRES structures | web | Picornaviridae, Flaviviridae, Discistroviridae, Retroviridae, Tombusviridae |
| Database of Bat-associated Viruses (DBatVir) | Bat viruses with details about their hosts and location | web | Bat viruses |
| European society for virology | Society promoting discussion and collaboration among scientists, organizing a congress every three years | web | All viruses |
| American society for virology | Society promoting discussion and collaboration among scientists, organizing an annual congress | web | all viruses |
| Plant viruses online | Classification, hosts and symptoms of plant viruses | web | Plant viruses |
| Virology history | description og historical developments that led to the determination of the structure and biological functions of viruses | web | Picornaviridae, Influenzavirus, plant viruses |
| Giantvirus.org | Resource on mimivirus (last update 2005) | web | Mimivirus, pandoravirus |
| Microbewiki: viral bioreaml | student-edited microbiology resource | web | all viruses |
| All the virology on the www | links to virology resources on the web | web | all viruses |
| ATIVS | Analysis tools for influenza virus surveillance | web | Influenza virus |
| AVPdb | Human viruses Resource of experimentally validated antiviral peptides | web | Human viruses |
| AVPpred | Antiviralpeptide prediction algorythm | web | all viruses | Base-By-Base | Software package to identify differences between genomes | download | all viruses |
| bNAber | Database of broadly neutralizing HIV antibodies | web | HIV |
| CAPIH | comparative host HIV-1 protein interaction network between human and model animals | web | HIV |
| CoVDB | Repository of annotated coronavirus genes/genomes | web | Coronavirus |
| DengueNet | For a global surveillance of Dengue fever and Dengue haemorrhagic fever | web | Dengue virus |
| Description of plant viruses (DPV) | Information about viruses, viroids and satellites of plants, fungi and protozoa. | web | Plant, funghi, protozoa viruses |
| Dr.VIS | Catalogs human disease-related viral integration sites | web | Human viruses |
| EpiFlu | Comprehensive collection of Influenza sequences containing associated clinical/epidemiological metadata | Web (login) | Influenza virus |
| euHCVdb | Resource computer-annotated sequences, protein sequences/structures and functional analyses tools (now succeeded by ViPR) | web | Hepatitis C virus |
| EuResist | For predicting response to anti-HIV therapy | web or download | HIV |
| FLAVIdB | Web portal combining antigenic data of flaviviruses and analysis tools | web | Flaviviruses |
| Flavitrack | Manually annotated database of flavivirus sequences | Inaccessible, Dec14 | Flaviviruses |
| FluGenome | For genotypoing influenza A virus and analyzing reassortment events | web | Influenza virus |
| FluTE | Influenza epidemic simulation model | download | Influenza virus |
| GATU (Genome Annotation Transfer Utility) | Annotation of viral genomes | web | all viruses |
| Geno2pheno | For predicting drug resistance in HIV-1, HBV and HCV | web | HIV-1, HBV and HCV |
| GIB-V | Platform for comparative analysis of viral genomes | Inaccessible dec14 | |
| GiRaF | Identification of influenza reassortments | download | Influenza virus |
| HBVdb | Provides access to computer-annotated sequences as well as generic (BLAST, FASTA, ClustalW) and specialized tools for annotation, genotyping and drug resistance profiling | web | HBV |
| HBVPathDB | Pathway information of HBV infection-related reactions | Inaccessible dec14 | HBV |
| HBVRegDB | Database for detection of regulatory elements | web | HBV |
| HepSEQ | Hosts molecular, clinical and epidemiological information as well as Sequence Matcher, Genotyper and Polymerase Annotator tools for HBV | web | HBV |
| HERVd | Repository of human endogenous retroviruses | web | HERV |
| HESAS | Database to understand the role of HERVs in the human genome | web | HERV |
| HIPdb | Repository of experimentally validated HIV inhibiting peptides | web | HIV |
| HIVCD | Tool for contamination screening in HIV sequence laboratory | download | HIV |
| HIV Positive Selection Mutation DB | Selection pressure maps of HIV protease and reverse transcriptase | web | HIV |
| HIVSIM | For comparing effectiveness of novel HIV therapy regimens | download | HIV |
| HIVsirDB | Repository of HIV inhibiting siRNAs | web | HIV |
| HIV Systems Biology | Houses Gene Overlapper, Replication Cycle site, GPS-Prot and AIDSVu tools | web | HIV |
| HPV-QUEST | Tool for genotyping HPV | web | HPV |
| HTLV-1 Molecular Epidemiology DB | For HTLV-1 sequence management and data mining | web | HTLV |
| HVDB | Database of hepatitis A/B/C/D/E virus sequences as well as provides a phylogenetic analysis tool | web | HAV, HBV, HCV, HDV, HEV |
| ICTV | Taxonomic classification and nomenclature of viruses | web | all viruses |
| IPDR | Designing primers/probes for influenza diagnostics | web | Influenza virus |
| IRD | Resource of influenza virus host-pathogen interactions as well | web | Influenza virus |
| ISED | Catalogs influenza sequence and epitope information of viruses from Asia | web | Influenza virus |
| IVDB | Hosts influenza sequence data, Q-filter system as well as BLAST, alignment, phylogenetic and sequence distribution tools | web | Influenza virus |
| jpHMM | To analyze recombinations in viruses | web and download | HIV, HBV |
| LANL HCV Database | Contains sequence data and immunological epitopes in HCV (now succeeded by ViPR) | web | HCV |
| LANL HFV Database | Houses annotated Hemorrhagic Fever Viruses sequences and several analysis tools | web | Hemorrhagic Fever Viruses |
| LANL HIV Database2 | Comprehensive resource on HIV sequences, immunological epitopes, drug resistance and vaccine trials | web | HIV |
| LearnCoil-VMF | Identifying coiled-coil-like motifs in viral membrane-fusion proteins | web | all viruses |
| Metavir | Web server for analysis of viral metagenomes (viromes) | web | metagenome |
| NCBI Genotyping Tool | Resource for genotyping of viral sequences | web | HIV, HBV, HTLV, Poliovirus |
| NCBI HIV-1, Human Interaction Database | Catalogs all interactions between HIV-1 and human proteins | web | HIV |
| NCBI Influenza Resource | Influenza virus standardized annotation, metadata based sequence retrieval and analysis tools | web | Influenza virus |
| NCBI Viral Genome Resource | Catalogue of all viral genomes with their proteins and references for all viral species. Contains more that 70,000 genomes | web | all viruses |
| NCBI Virus Variation Resource | Ebolavirus, MERS coronavirus, Dengue, West Nile-standardized annotation, metadata based sequence retrieval and analysis tools | web | Ebolavirus, MERS coronavirus, Dengue, West Nile virus |
| OpenFluDB | Isolate-centric database for influenza virus (contains information about virus type, host and collection date/place) | web | Influenza virus |
| Paparazzi | Perl script to reconstruct entire viral genome from virus-derived siRNAs | Inaccessible, Fev15 | NGS |
| PaVE | Hosts annotated papillomavirus genomes and protein sequence/structures | web | HPV |
| PBRC | Comprehensive Poxviridae informational and analytical resource (now merged into ViPR) | web | Poxviridae |
| PHACCS | To assess the diversity of uncultured/environmental viral communities | download | metagenome |
| PhEVER | Houses evolutionary and phylogenetic information to analyze the nature of virus-virus and virus-host lateral gene transfers | web | all viruses |
| phiSITE | Database of gene regulation in bacteriophages | web | phages |
| PhyloType | To analyze large phylogenies | web and download | Phylogeny |
| PIRSpred | For HIV-1 protein-inhibitor resistance/susceptibility prediction | web | HIV |
| PrimerHunter | Primer designing tool for virus subtyping | web and download | all viruses |
| PriSM | Tool to select optimal primers for amplification of viral genomes | web | all viruses |
| RetroTector | Detection of retroviral sequences in vertebrate genomes | web | Retroviridae |
| RNA Virus Database | Devoted to RNA viruses | web | RNA viruses |
| RotaC | Genotyping tool for group A rotaviruses | web | Rotavirus |
| SCUEAL | Prediction of HIV-1 subtypes | web | HIV |
| SeqMap 2.0 | Identifying integration sites from LM-PCR, LAM-PCR and nrLAM-PCR analysis | web | Integrated virus |
| siVirus | Antiviral siRNA design software | web | HIV, SARS, Influenza, HCV |
| SQUAT | Examining the quality of HIV-1 PR/RT sequences | download | HIV |
| SSE | Nucleotide and amino acid sequence analysis platform | download | all viruses |
| Stanford HIV Drug Resistance DB | Contains genotype-treatment, genotype-phenotype and genotype-outcome correlation data | web | HIV |
| STAR | Subtyping tool for HIV-1 and HBV | web | HIV, HBV |
| Subviral RNA Database | For research/analysis of viroids, satellite RNAs, satellites viruses and human hepatitis delta virus | web | RNA viruses |
| SugarBind | Pathogen glucide/carbohydrate-binding database | web | |
| VaZyMolO | BLAST tool for defining/classifying viral protein modules | web | all viruses |
| VBRC | Viral resource of informational and analytical tools (now merged into ViPR) | web | Arenaviridae, Bunyaviridae, Flaviridae, Filoviridae, Paramyxoviridae, Poxviridae, Togaviridae |
| vFitness | To estimate HIV-1 fitness (replication rate) | web | HIV |
| VGO | Annotation of complete viral genomes especially large poxviruses | web | poxviridae |
| VIDA | Organizes homologous protein families from animal virus genomes | web | Arteriviridae, Poxviridae, Coronaviridae, Herpesviridae, Papillomaviridae |
| VIGOR | Gene prediction program | web | RNA viruses |
| VIPERdb | Database for icosahedral virus capsid structures | web | All viruses |
| ViPR | Integrated repository of data (sequences, protein structures, epitopes, clinical/surveillance metadata) and analysis tools (BLAST, alignment, phylogeny) for multiple virus families | web | Caliciviridae, Coronaviridae, Flaviviridae, Hepeviridae, Picornaviridae, Togaviridae, Arenaviridae, Bunyaviridae, Filoviridae, Paramyxoviridae, Rhabdoviridae, Reoviridae, Herpesviridae, Poxviridae |
| VIPR | For detecting recombinant and non-recombinant viruses hybridized to diagnostic microarray | download | all viruses |
| Viral IRES Prediction System (VIPS) | Prediction of viral IRESs | web | all viruses |
| ViralFusionSeq | To discover integration events by combining soft-clipping information, read-pair analysis and targeted de novo assembly | download | all viruses |
| ViralZone | Fact sheets on all known virus families/genera with sequence data | web | all viruses |
| VIRAPOPS | Forward simulator to model specific RNA virus functions | download | RNA virus |
| ViReMa | Algorithm for detection of recombination junctions in viral genomes | download | all viruses |
| VirHostNet | Resource of virus-host interaction networks coupled to their functional annotation | web | all viruses |
| Vir-Mir db | Catalogs potential viral miRNA hairpins and allows prediction of viral miRNA target genes | web | all viruses |
| ViroBLAST | Extends utility of BLAST to query against multiple databases and user-customized datasets | web and download | all viruses |
| VirOligo | Repository of virus-specific oligonucleotides | web | all viruses |
| VIROME | Pipeline for classification of viral metagenomic sequences | web | metagenome |
| viRome | R package for analysis of viral small RNA sequence datasets | download | all viruses |
| VIRsiRNAdb | Curated database of siRNA/shRNA targeting 42 important human viruses | web | Human viruses |
| VIRsiRNApred | Viral siRNA efficacy prediction tool | web | all viruses |
| VirusFinder | Software for detecting integration sites by blending SVdetect with CREST | download | NGS |
| Virus-Genotyping Tools | High-throughput genotyping of recombinant and nonrecombinant viruses | web | HIV, HTLV, HBV, HCV, KSHV, HPV |
| VirusHunter | Pipeline for detection of novel/known viruses from various specimens | download | metagenome |
| VirusMINT | Hosts interactions between viral and human proteins | web | |
| VirusSeq | For finding integration events using discordant read-pair information | download | all viruses |
| Visitor | Perl script for analysis of viral siRNA datasets from Illumina sequencing platform | download | Drosophila viruses |
| ViTa | Houses known host/viral miRNAs and known/putative host miRNA targets | web | all viruses |
| VMGAP | Pipeline for functional annotation of metagenomic data | method | metagenome |
| ZCURVE_V | Gene-finding tool for viral genomes | web and download | all viruses |
| Paleovirology | This website aims to provide a stable repository for the endogenous viruses, and provides paleovirus reference sequences for retroviruses | web | all endogenous viruses |
| ViRBase | visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection | web | all viruses |
| ViRAD | Virus (re-)annotation database; adds newly identified ORFs to virus sequences | web | all viruses |
| VirAmp | fast virus genome assembly pipeline designed for extremely high coverage NGS data | web | all viruses |
| PaVE | Papillomavirus Episteme: resource with reference sequences, annotation and analysis tools | web | Papillomaviruses |
| VirusDetect | An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. | web | Plant viruses |
| ScienceofHIV | Animation showing some key steps of HIV life cycle | Web | HIV |
| Virus orthologous groups VOGDB | Orthologous groups from RefSeq viral genomes | Web | all viruses |
| Virus host database | data represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts | Web | all viruses |
| Bacteriophage genomes | Table of >9000 Complete Bacteriophage genomes extracted from Genbank | Web | phages |
| Genome detective tool | The Virus tool assigns taxonomic names to sequences from eukaryotic viruses and phages. | Web | all viruses, NGS, Metagenomics |
Sources: -Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research For further details and to compare/select the most suitable tools to carry out a desired task refer to the aforementioned paper. -2014 NAR Database Summary Paper #html