# Virus Pathogen Database and Analysis Resource > Mediated Wiki article. Canonical URL: https://mediated.wiki/source/Virus_Pathogen_Database_and_Analysis_Resource > Markdown URL: https://mediated.wiki/source/Virus_Pathogen_Database_and_Analysis_Resource.md > Source: https://en.wikipedia.org/wiki/Virus_Pathogen_Database_and_Analysis_Resource > Source revision: 1342115794 > License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) {{More citations needed|date=October 2011}} {{Infobox recurring event |name = VIPR BRC |logo = |image = VIPR_logo.png |caption = VIPR logo |location = |years_active = |dates = |genre = |website = [http://www.viprbrc.org/ www.viprbrc.org] }} The '''Virus Pathogen Database and Analysis Resource (ViPR)''' [http://www.viprbrc.org/ Virus Pathogen Database and Analysis Resource (ViPR)]{{cite journal | doi=10.1093/nar/gkr859 | title=ViPR: An open bioinformatics database and analysis resource for virology research | year=2012 | last1=Pickett | first1=Brett E. | last2=Sadat | first2=Eva L. | last3=Zhang | first3=Yun | last4=Noronha | first4=Jyothi M. | last5=Squires | first5=R. Burke | last6=Hunt | first6=Victoria | last7=Liu | first7=Mengya | last8=Kumar | first8=Sanjeev | last9=Zaremba | first9=Sam | last10=Gu | first10=Zhiping | last11=Zhou | first11=Liwei | last12=Larson | first12=Christopher N. | last13=Dietrich | first13=Jonathan | last14=Klem | first14=Edward B. | last15=Scheuermann | first15=Richard H. | journal=Nucleic Acids Research | volume=40 | issue=Database issue | pages=D593–D598 | pmid=22006842 | pmc=3245011 }}{{cite journal | doi=10.3390/v4113209 | doi-access=free | title=Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community | year=2012 | last1=Pickett | first1=Brett | last2=Greer | first2=Douglas | last3=Zhang | first3=Yun | last4=Stewart | first4=Lucy | last5=Zhou | first5=Liwei | last6=Sun | first6=Guangyu | last7=Gu | first7=Zhiping | last8=Kumar | first8=Sanjeev | last9=Zaremba | first9=Sam | last10=Larsen | first10=Christopher | last11=Jen | first11=Wei | last12=Klem | first12=Edward | last13=Scheuermann | first13=Richard | journal=Viruses | volume=4 | issue=11 | pages=3209–3226 | pmid=23202522 | pmc=3509690 }} is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for viral pathogens in the U.S. [National Institute of Allergy and Infectious Diseases](/source/National_Institute_of_Allergy_and_Infectious_Diseases) (NIAID) Category A-C Priority Pathogen lists for biodefense research, and other viral pathogens causing emerging/reemerging infectious diseases. ViPR is one of the five [Bioinformatics Resource Centers](/source/Bioinformatics_Resource_Centers) (BRC) funded by [NIAID](/source/NIAID), a component of the [National Institutes of Health](/source/National_Institutes_of_Health) (NIH), which is an agency of the [United States Department of Health and Human Services](/source/United_States_Department_of_Health_and_Human_Services). ==Virus families covered in ViPR== The ViPR database includes genomes from these viral families: [Arenaviridae](/source/Arenaviridae), [Bunyaviridae](/source/Bunyaviridae), [Caliciviridae](/source/Caliciviridae), [Coronaviridae](/source/Coronaviridae), [Filoviridae](/source/Filoviridae), [Flaviviridae](/source/Flaviviridae), [Hepeviridae](/source/Hepeviridae), [Herpesviridae](/source/Herpesviridae), [Paramyxoviridae](/source/Paramyxoviridae), [Picornaviridae](/source/Picornaviridae), [Poxviridae](/source/Poxviridae), [Reoviridae](/source/Reoviridae), [Rhabdoviridae](/source/Rhabdoviridae), and [Togaviridae](/source/Togaviridae). == Data types in ViPR == * [Genomes](/source/Genomes) * Genome [annotations](/source/annotations) * Genes & [proteins](/source/proteins) * Predicted protein domains and motifs * Immune [epitopes](/source/epitopes) * Sequence Features {{cite journal | doi=10.1128/JVI.06901-11 | title=Influenza Virus Sequence Feature Variant Type Analysis: Evidence of a Role for NS1 in Influenza Virus Host Range Restriction | year=2012 | last1=Noronha | first1=Jyothi M. | last2=Liu | first2=Mengya | last3=Squires | first3=R. Burke | last4=Pickett | first4=Brett E. | last5=Hale | first5=Benjamin G. | last6=Air | first6=Gillian M. | last7=Galloway | first7=Summer E. | last8=Takimoto | first8=Toru | last9=Schmolke | first9=Mirco | last10=Hunt | first10=Victoria | last11=Klem | first11=Edward | last12=García-Sastre | first12=Adolfo | last13=McGee | first13=Monnie | last14=Scheuermann | first14=Richard H. | journal=Journal of Virology | volume=86 | issue=10 | pages=5857–5866 | pmid=22398283 | pmc=3347290 }} * Orthologous protein clusters * 3D [protein structure](/source/protein_structure) * Clinical metadata * Host factor data == Analysis and visualization tools in ViPR == * BLAST: provides a variety of custom ViPR databases to identify the most related sequence(s) * Short Peptide Search: allows users to find any peptide sequence using exact, fuzzy, or pattern matching * Sequence Variation Analysis ([Single-nucleotide polymorphism] SNP): calculates sequence variation existing in the specified sequences * Metadata-driven Comparative Analysis Tool for Sequences (Meta-CATS): an automated comparative statistical analysis to identify positions throughout a [multiple sequence alignment](/source/multiple_sequence_alignment) that significantly differ between groups of sequences possessing specific phenotypic characteristic * Multiple Sequence Alignment: aligns small genomes, gene/protein sequences or large viral genome sequences using one of several algorithm best-suited for the specific job submission * Sequence Alignment Visualization: uses JalView for sequence alignment visualization * Phylogenetic Tree Generation: calculates a tree using one of several available algorithms and evolutionary models * Phylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree using the Archaeopteryx viewer * GBrowse: provides genome browsing capability for large DNA viral genomes (Herpesviridae and Poxviridae) with integration of ViPR Sequence Features for Vaccinia virus * [Sequence Feature Variant Type](/source/Sequence_Feature_Variant_Type) (SFVT) analysis: provides a centralized repository of functional regions and automatically calculates all observed sequence variation within each defined region * 3D Protein Structure Visualization: integrates PDB protein structure files with ViPR Sequence Features when applicable and provides an interactive 3D protein structure viewer using Jmol * Genome Annotator (GATU): allows users to annotate new genome sequences provided by the user * Genotype Determination and Recombination Detection: predicts the genotype for user-provided sequences and identifies possible sites of recombination for viruses in the family Flaviviridae * PCR Primer Design: allows the user to automatically predict ideal primers based on a sequence and specified parameters * ReadSeq: converts between various sequence formats * Sequence Feature Submission Tool: allows users to define a Sequence Feature by filling out a webform * External Analysis Tools: displays a list and description of third-party tools for more specialized analyses * Personal Workbench to save and share data and analysis == References == {{Reflist}} ==External links== * {{official website|http://www.viprbrc.org/|ViPR BRC}} * [https://web.archive.org/web/20130128030912/http://www.niaid.nih.gov/LabsAndResources/resources/dmid/brc/Pages/default.aspx Bioinformatics Resource Centers] The NIAID page describing the goals and activities of the BRCs Category:Biological databases Category:Pathogen genomics --- Adapted from the Wikipedia article [Virus Pathogen Database and Analysis Resource](https://en.wikipedia.org/wiki/Virus_Pathogen_Database_and_Analysis_Resource) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Virus_Pathogen_Database_and_Analysis_Resource?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.