Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community
Open Access
- 19 November 2012
- Vol. 4 (11), 3209-3226
- https://doi.org/10.3390/v4113209
Abstract
Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.Keywords
This publication has 46 references indexed in Scilit:
- NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policyNucleic Acids Research, 2011
- ViPR: an open bioinformatics database and analysis resource for virology researchNucleic Acids Research, 2011
- The RCSB Protein Data Bank: redesigned web site and web servicesNucleic Acids Research, 2010
- Search and clustering orders of magnitude faster than BLASTBioinformatics, 2010
- Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosisHuman Molecular Genetics, 2009
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- ProtTest: selection of best-fit models of protein evolutionBioinformatics, 2005
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997