TABLE 2.
List and comparison of virus-centered resources
| Species | Resourcea | No. of genomes | No. of sequences | Specific featureb | CIc | Accessd |
|---|---|---|---|---|---|---|
| Dengue virus | NCBI-VVR | 3,204 | 13,125 | Comprehensive sequence database with analysis tools | 3.4 | W |
| DengueNet | For global surveillance of DF/DHF | 0.2 | W | |||
| HBV | SeqHepB | 3,391 | For determination of genotype and resistance-associated mutations | 7.4 | ||
| HBVdb | ∼4,000 | 46,667 | Hosts all known sequences and generic/specialized tools | 2.1 | W | |
| HepSEQ | 40 | 4,296 | Focuses on HBV variants from patients | 2.0 | W | |
| HBVRegDB | For detection of regulatory elements | 1.9 | W | |||
| HCV | LANL HCV database | 1,656e | 155,260 | Contains sequence data and immunological epitopes | 24.3 | W |
| euHCVdb | 62 | 96,645 | Resource of sequences, protein structures, analysis tools | 12.4 | W | |
| HFV | LANL HFV database | ∼6,000 | 63,773 | Houses annotated sequences and several analysis tools | 0.8 | W |
| HIV | Stanford HIV drug resistance DB | 157,681 | Drug resistance mutations/predictions in HIV-1 | 14.6 | W | |
| LANL HIV database | 4,631 | 584,970 | Hosts sequences, epitopes, mutations, clinical trials, tools | 7.0 | W | |
| bNAber | Database of broadly neutralizing antibodies | 4.8 | W | |||
| SQUAT | Evaluating quality of HIV-1 PR/RT sequences | 3.9 | D | |||
| EuResist | 140,104 | For predicting response to therapy and subtyping | 2.7 | W, D | ||
| HIV positive selection mutation DB | 50,634 | Provides selection pressure maps of PR/RT | 2.4 | W | ||
| vFitness | Assessment of HIV-1 replication rate | 1.5 | W | |||
| PIRSpred | Prediction of HIV-1 drug resistance | 1.3 | W | |||
| HIVCD | Tool for contamination detection in HIV laboratory | 1.0 | D | |||
| HIV Systems Biology | Protein interactions, host-gene data, and epidemic maps | 0.9 | W | |||
| HIVSIM | Assesses effectiveness of novel therapy regimens | 0.4 | D | |||
| SCUEAL | For subtyping HIV-1 | 0.2 | W | |||
| HTLV-1 | HTLV-1 molecular epidemiology DB | 16 | 2,571 | Stores annotated proviral sequences | 1.3 | W |
| Influenza virus | NCBI-IVR | 17,784 | 297,660 | Houses sequence data and analysis tools | 78.5 | W |
| FluTE | Influenza epidemic simulation model | 23.0 | D | |||
| IRD | 17,988 | 306,164 | Host-pathogen interactions and analysis tools | 22.6 | W | |
| FluGenome | 7,135 | 118,810 | For genotyping influenza A virus | 8.1 | W | |
| IVDB | ∼3,000 | 43,875 | Catalogs sequences and geographic distribution of genotypes | 5.6 | W | |
| EpiFlu | 16,144 | 367,672 | Sequences and associated clinical/epidemiological data | 4.3 | W | |
| GiRaF | For detection of reassortments | 3.6 | D | |||
| OpenFluDB | 11,443 | 232,688 | Isolate-centered inventory | 2.4 | W | |
| ISED | 181,552 | Catalogs influenza virus sequences/epitopes from Asia | 1.7 | W | ||
| IPDR | 305,990 | Primer designing tool for diagnostics | 1.3 | W | ||
| ATIVS | Tool for influenza virus surveillance | 1.2 | W | |||
| Papillomavirus | PaVE | 274 | 2,994 | Hosts annotated genomes and proteins sequences/structures | 6.7 | W |
| Poxvirus | PBRC (later merged into ViPR) | 328 | 22,289 | 4.6 | W | |
| West Nile virus | NCBI-VVR | 627 | 2,438 | Comprehensive sequence database with analysis tools | 3.4 | W |
a
For each virus, resources have been listed in order of decreasing citation index values (numbers of citations per year).
b
DF, dengue fever; DHF, dengue hemorrhagic fever; PR, protease; RT, reverse transcriptase.
c
CI, citation index.
d
W, Web based; D, downloadable; W, D, both Web based and downloadable.
e
Many genomes classified as “complete genome” have been listed as “partial genome” by euHCVdb.