ViPR: an Open Bioinformatics Database and Analysis Resource for Virology Research

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Oct 19

PMID 22006842

Citations 397

Authors

Brett E Pickett

Eva L Sadat

Yun Zhang

Jyothi M Noronha

R Burke Squires

Victoria Hunt

Mengya Liu

Sanjeev Kumar

Sam Zaremba

Zhiping Gu

Liwei Zhou

Christopher N Larson

Jonathan Dietrich

Edward B Klem

Richard H Scheuermann

Affiliations

Soon will be listed here.

Abstract

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal 'Workbenches' for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

Citing Articles

VITALdb: to select the best viroinformatics tools for a desired virus or application.

Koul M, Kaushik S, Singh K, Sharma D Brief Bioinform. 2025; 26(2).

PMID: 40063348 PMC: 11892104. DOI: 10.1093/bib/bbaf084.

Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.

Langenfeld K, Hegarty B, Vidaurri S, Crossette E, Duhaime M, Wigginton K Nucleic Acids Res. 2025; 53(5).

PMID: 40036505 PMC: 11878531. DOI: 10.1093/nar/gkaf118.

Detection and characterization of bovine coronavirus and rotavirus in calves in Ethiopia.

Redda Y, Adamu H, Bergholm J, Lindahl J, Blomstrom A, Berg M BMC Vet Res. 2025; 21(1):122.

PMID: 40022093 PMC: 11869714. DOI: 10.1186/s12917-025-04563-9.

Advances of computational methods enhance the development of multi-epitope vaccines.

Wei Y, Qiu T, Ai Y, Zhang Y, Xie J, Zhang D Brief Bioinform. 2025; 26(1).

PMID: 39951549 PMC: 11827616. DOI: 10.1093/bib/bbaf055.

Genomic analysis of DS-1-like human rotavirus A strains uncovers genetic relatedness of NSP4 gene with animal strains in Manhiça District, Southern Mozambique.

Manjate F, Joao E, Mwangi P, Chirinda P, Mogotsi M, Garrine M Sci Rep. 2024; 14(1):30705.

PMID: 39730435 PMC: 11680989. DOI: 10.1038/s41598-024-79767-4.

References

. From the Centers for Disease Control and Prevention. Severe acute respiratory syndrome--Taiwan, 2003. JAMA. 2003; 289(22):2930-2. DOI: 10.1001/jama.289.22.2930. View

Tcherepanov V, Ehlers A, Upton C . Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome. BMC Genomics. 2006; 7:150. PMC: 1534038. DOI: 10.1186/1471-2164-7-150. View

Greene J, Collins F, Lefkowitz E, Roos D, Scheuermann R, Sobral B . National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007; 75(7):3212-9. PMC: 1932942. DOI: 10.1128/IAI.00105-07. View

Clamp M, Cuff J, Searle S, Barton G . The Jalview Java alignment editor. Bioinformatics. 2004; 20(3):426-7. DOI: 10.1093/bioinformatics/btg430. View

. Imported dengue--United States, 1999 and 2000. MMWR Morb Mortal Wkly Rep. 2002; 51(13):281-3. View

Bao Y, Federhen S, Leipe D, Pham V, Resenchuk S, Rozanov M . National center for biotechnology information viral genomes project. J Virol. 2004; 78(14):7291-8. PMC: 434121. DOI: 10.1128/JVI.78.14.7291-7298.2004. View

Posada D, Crandall K . MODELTEST: testing the model of DNA substitution. Bioinformatics. 1999; 14(9):817-8. DOI: 10.1093/bioinformatics/14.9.817. View

Waterhouse A, Procter J, Martin D, Clamp M, Barton G . Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25(9):1189-91. PMC: 2672624. DOI: 10.1093/bioinformatics/btp033. View

Zmasek C, Eddy S . ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics. 2001; 17(4):383-4. DOI: 10.1093/bioinformatics/17.4.383. View

10.

Stamatakis A, Ludwig T, Meier H . RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2004; 21(4):456-63. DOI: 10.1093/bioinformatics/bti191. View

11.

. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2010; 39(Database issue):D214-9. PMC: 3013648. DOI: 10.1093/nar/gkq1020. View

12.

Lefkowitz E, Upton C, Changayil S, Buck C, Traktman P, Buller R . Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res. 2004; 33(Database issue):D311-6. PMC: 540064. DOI: 10.1093/nar/gki110. View

13.

Thomson G, Marthandan N, Hollenbach J, Mack S, Erlich H, Single R . Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput. 2009; :359-70. PMC: 2958177. DOI: 10.1142/9789814295291_0038. View

14.

Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

15.

. Outbreak of West Nile-like viral encephalitis--New York, 1999. MMWR Morb Mortal Wkly Rep. 1999; 48(38):845-9. View

16.

Oliveira M, Araujo J, Costa Ferreira Jr O, Ferreira D, Lima D, Santos F . Two lineages of dengue virus type 2, Brazil. Emerg Infect Dis. 2010; 16(3):576-8. PMC: 3322019. DOI: 10.3201/eid1603.090996. View

17.

Bennett S, Holmes E, Chirivella M, Rodriguez D, Beltran M, Vorndam V . Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction. J Gen Virol. 2006; 87(Pt 4):885-893. DOI: 10.1099/vir.0.81309-0. View

18.

Larsen M, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M . Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics. 2007; 8:424. PMC: 2194739. DOI: 10.1186/1471-2105-8-424. View

19.

Ha D, Tien N, Huong V, Loan H, Thang C . Dengue epidemic in southern Vietnam, 1998. Emerg Infect Dis. 2000; 6(4):422-5. PMC: 2640906. DOI: 10.3201/eid0604.000421. View

20.

Vita R, Zarebski L, Greenbaum J, Emami H, Hoof I, Salimi N . The immune epitope database 2.0. Nucleic Acids Res. 2009; 38(Database issue):D854-62. PMC: 2808938. DOI: 10.1093/nar/gkp1004. View