TABLE 3.
Categorization and comparison of resources based on specific application
| Application | Resourcea | Specific feature(s)/organism(s) (if any)b | CIc | Webd |
|---|---|---|---|---|
| Metagenomics | PHACCSe | 13.1 | W | |
| Metavir | 10.1 | W | ||
| VIROME | 6.9 | W | ||
| VMGAP | 3.5 | |||
| Primer designing | ViralORFeome | For designing ORF-specific primers | 6.9 | W |
| PrimerHunter | For subtype identification | 2.6 | W, D | |
| VirOligo | Repository of virus-specific oligonucleotides | 1.7 | W | |
| IPDR | For influenza diagnostics | 1.3 | W | |
| PriSM | For amplification of viral genomes | 0.9 | W | |
| Protein-protein interaction | NCBI-HHPID | Catalogs human–HIV-1 interactions | 28.4 | W |
| VirusMINT | 16.5 | W | ||
| VirHostNet | 11.3 | W | ||
| CAPIH | Hosts human–animal–HIV-1 interactions | 1.1 | W | |
| HIV systems biology (GPS-Prot) | Resource for human–HIV interactions | 0.9 | W | |
| siRNA analysis | Paparrazi | Reconstruct viral genome from siRNAs | 6.8 | D |
| siVirus | For designing antiviral RNA (HCV, HIV-1, IV, SARS-CoV) | 3.4 | W | |
| VIRsiRNAdb | Database of siRNA/shRNA targeting 42 viruses | 3.2 | W | |
| HIVsirDB | Repository of HIV-inhibiting siRNAs | 3.2 | W | |
| Visitor | Analysis of viral siRNAs from Illumina platform | 0.4 | D | |
| viRome | R package for analysis of small RNA sequences | 0 | D | |
| VIRsiRNApred | Viral siRNA efficacy prediction tool | 0 | W | |
| Structural analysis | VIPERdb | Database of icosahedral virus capsid structures | 23.8 | W |
| LearnCoil-VMFe | 10.3 | W | ||
| Subtyping/genotyping | RotaC | Group A rotavirus | 19.5 | W |
| Geno2pheno | HBV, HCV, HIV-1 | 17.9 | W | |
| Stanford HIV drug resistance DB | HIV-1 | 14.6 | W | |
| NCBI genotyping tool | HBV, HCV, HIV, HTLV, PV | 14.4 | W | |
| Virus genotyping tools | HBV, HCV, HHV8, HIV, HPV, HTLV | 8.3 | W | |
| FluGenome | Influenza A virus | 8.1 | W | |
| SeqHepB | HBV | 7.4 | ||
| STAR | HBV, HIV | 4.9 | W | |
| EuResist | HIV-1 | 2.7 | W, D | |
| PrimerHunter | Primer design for subtype identification | 2.6 | W, D | |
| HBVdb | HBV | 2.1 | W | |
| HepSEQ | HBV | 2.0 | W | |
| SCUEAL | HIV-1 | 0.2 | W | |
| HPV-QUEST | HPV | 0 | W | |
| Viral integration | VirusSeq | 6.4 | D | |
| ViralFusionSeq | 4.8 | D | ||
| VirusFinder | 4.4 | D | ||
| SeqMap 2.0 | 3.0 | W | ||
| Dr.VIS | Database of human disease-related VIS | 2.6 | W | |
| Viral recombination | jpHMM | HBV, HIV-1 | 7.7 | W, D |
| ViReMa | 2.0 | D | ||
| SeLOX | 1.6 | W | ||
| VIPR HMM | 0 | D | ||
| Miscellaneousf | Virus-PLoc | Prediction of subcellular localization of proteins | 14.6 | W |
| SSE | Nucleotide/protein sequence analysis platform | 13.3 | D | |
| VirusHunter | Detection of novel/known viruses from specimens | 8.0 | D | |
| RetroTector | Identification of retroviral sequences in vertebrates | 7.9 | W | |
| ViPR | Repository of data and analysis tools for viruses | 7.6 | W | |
| Subviral RNA database | Toolbox for viroids, satellite RNAs, and HDV | 6.8 | W | |
| ViroBLAST | For BLAST searches against multiple databases and user's data set | 6.7 | W, D | |
| ViralZone | Fact sheets on all known virus families/genera | 6.0 | W | |
| ViTa | Houses host/viral miRNAs and known/putative targets | 5.9 | W | |
| VIDA | Organizes ORFs from animal virus genomes | 5.9 | W | |
| GATU | Annotation of viral genomes | 5.6 | W | |
| Vir-Mir db | Prediction of viral miRNA target genes | 5.6 | W | |
| HVDB | Database of hepatitis A, B, C, D, and E virus sequences | 5.3 | W |
a
For each application, resources have been listed in order of decreasing citation index values (numbers of citations per year).
b
HDV, hepatitis delta virus; HHV, human herpesvirus; HTLV, human T-lymphotropic virus; HPV, human papillomavirus; IV, influenza virus; PV, poliovirus; SARS-CoV, SARS coronavirus; VIS, viral integration sites.
c
CI, citation index.
d
W, Web based; D, downloadable; W, D, both Web based and downloadable.
e
Currently inaccessible.
f
Resources with CI > 5 (the virus-centered tools with CI > 5 listed in Table 2 have been excluded).