Virus Bioinformatics Tools

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations, including 2502 viral proteomes. eggNOG offers online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets.

J. Huerta-Cepas, D. Szklarczyk, D. Heller, A. Hernández-Plaza, S. K. Forslund, H. Cook, D. R. Mende, I. Letunic, T. Rattei, L. J. Jensen, C. von Mering, and P. Bork. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res, vol. 47, iss. D1, p. D309–D314, 2018.
10.1093/nar/gky1085

EpiFlu™ is the world's most complete collection of genetic sequence data of influenza viruses and related clinical and epidemiological data. EpiFlu™ is tailored to the needs of influenza researchers from both the human and the veterinary fields. The data is publicly accessible but not Public Domain (GISAID does not remove nor waive any preexisting rights).

Y. Shu and J. McCauley. GISAID: global initiative on sharing all influenza data – from vision to reality. Eurosurveillance, vol. 22, iss. 13, 2017.
10.2807/1560-7917.es.2017.22.13.30494

The HCV database group strives to present HCV-associated, hand-annotated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.

C. Kuiken, K. Yusim, L. Boykin, and R. Richardson, “The Los Alamos hepatitis C sequence database.,” Bioinformatics, vol. 21, p. 379–384, 2005.
10.1093/bioinformatics/bth485

HSV-1 genome browser software for easy accessibility of the complete viral transcriptome and translatome of herpes simplex virus 1 (HSV-1) during lytic infection with base-pair resolution by computational integration of multi-omics data. 201 viral transcripts and 284 open reading frames (ORFs), including 46 novel large ORFs. Viral gene expression and all data can be visually examined from whole genome to single-nucleotide resolution.

F. Erhard and C. Jürges. Hsv-1 viewer, Zenodo, 2019.
10.5281/ZENODO.3465873

A. W. Whisnant, C. S. Jürges, T. Hennig, E. Wyler, B. Prusty, A. J. Rutkowski, A. L’hernault, L. Djakovic, M. Göbel, K. Döring, J. Menegatti, R. Antrobus, N. J. Matheson, F. W. H. Künzig, G. Mastrobuoni, C. Bielow, S. Kempa, C. Liang, T. Dandekar, R. Zimmer, M. Landthaler, F. Grässer, P. J. Lehner, C. C. Friedel, F. Erhard, and L. Dölken. Integrative functional genomics decodes herpes simplex virus 1. Nat Commun, vol. 11, p. 2038, 2020.
10.1038/s41467-020-15992-5

The International Committee on Taxonomy of Viruses (ICTV) authorises and organises the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed an universal taxonomic-scheme for viruses.

IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200,000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences.

I. Almansour, M. Alhagri, R. Alfares, M. Alshehri, R. Bakhashwain, and A. Maarouf. IRAM: virus capsid database and analysis resource. Database, vol. 2019, 2019.
10.1093/database/baz079

MMRdb is a web central database and analysis resource for measles, mumps, and rubella viruses. Users can search viruses at gene level and obtain sequence information based on gene product, geographic location, year, or host. The MMRdb also catalogs experimentally verified B cells and T cells antigenic epitopes data. A set of computation tools such as multiple sequence alignment, Geo Chart, and sequence similarity BLAST search has been implemented in a user-friendly database.

I. Almansour and M. Alhagri. MMRdb: measles, mumps, and rubella viruses database and analysis resource. Infect Genet Evol, vol. 75, p. 103982, 2019.
10.1016/j.meegid.2019.103982

OrthoDB samples the diversity of 7963 viruses and provides their evolutionary and functional ortholog annotations, as well as allowing user data mapping, and free stand-alone software for custom analyses.

The ViPR database integrates various types of data for multiple virus families. You can search the comprehensive database for sequences & strains, immune epitopes, 3D protein structures, host factor data, antiviral drugs, plasmid data. Further you can analyze the data online using sequence alignment, phylogenetic tree reconstruction, sequence variation (SNP), metadata-driven comparative analysis and BLAST.

B. E. Pickett, E. L. Sadat, Y. Zhang, J. M. Noronha, B. R. Squires, V. Hunt, M. Liu, S. Kumar, S. Zaremba, Z. Gu, L. Zhou, C. N. Larson, J. Dietrich, E. B. Klem, and R. H. Scheuermann. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res, vol. 40, iss. D1, p. D593–D598, 2011.
10.1093/nar/gkr859