The Virus Pathogen Database and Analysis Resource (ViPR) 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 The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services. NIAID's mis ...

(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 (BRC) funded by NIAID, a component of the

National Institutes of Health The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Service ...

(NIH), which is an agency of the

United States Department of Health and Human Services The United States Department of Health and Human Services (HHS) is a cabinet-level executive branch department of the US federal government created to protect the health of the US people and providing essential human services. Its motto is ...

Virus families covered in ViPR

The ViPR database includes genomes from these viral families: Arenaviridae,

Bunyaviridae ''Bunyaviricetes'' is a class of segmented negative-strand RNA viruses with mainly tripartite genomes. Member viruses infect arthropods, plants, protozoans, and vertebrates. The name ''Bunyaviricetes'' derives from Bunyamwera, where the virus B ...

Caliciviridae The ''Caliciviridae'' are a family of "small round structured" viruses, members of Class IV of the Baltimore scheme. Caliciviridae bear resemblance to enlarged picornavirus and was formerly a separate genus within the picornaviridae. They are ...

Coronaviridae ''Coronaviridae'' is a family (biology), family of Viral envelope, enveloped, positive-strand RNA viruses which infect fish, amphibians, birds, and mammals. The group includes the subfamilies ''Letovirinae,'' ''Orthocoronavirinae'', and ''Pitovir ...

Filoviridae ''Filoviridae'' () is a International Committee on Taxonomy of Viruses, family of RNA virus#Group_V_–_negative-sense_ssRNA_viruses, single-stranded negative-sense RNA viruses in the order (biology), order ''Mononegavirales''. Two members of the ...

Flaviviridae ''Flaviviridae'' is a family of Viral envelope, enveloped positive-strand RNA viruses which mainly infect mammals and birds. They are primarily spread through arthropod vector (epidemiology), vectors (mainly ticks and mosquitoes). The family gets ...

, Hepeviridae,

Herpesviridae ''Orthoherpesviridae'', previously named and more widely known as ''Herpesviridae'', is a large family of DNA viruses that cause infections and certain diseases in animals, including humans. The members of this family are commonly known as herp ...

Paramyxoviridae ''Paramyxoviridae'' (from Ancient Greek, Greek ''para-'' “by the side of” and ''myxa'' “mucus”) is a family of negative-strand RNA viruses in the order ''Mononegavirales''. Vertebrates serve as natural hosts. Diseases associated with this ...

Picornaviridae Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm ...

Poxviridae ''Poxviridae'' is a family of double-stranded DNA viruses. Vertebrates and arthropods serve as natural hosts. The family contains 22 genera that are assigned to two subfamilies: ''Chordopoxvirinae'' and ''Entomopoxvirinae''. ''Entomopoxvirinae'' ...

Reoviridae ''Reovirales'' is an order of double-stranded RNA viruses. Member viruses, called reoviruses, have a wide host range, including vertebrates, invertebrates, plants, protists and fungi. They lack lipid envelopes and package their segmented geno ...

Rhabdoviridae ''Rhabdoviridae'' is a family of negative-strand RNA viruses in the order ''Mononegavirales''. Vertebrates (including mammals and humans), invertebrates, plants, fungi and protozoans serve as natural hosts. Diseases associated with member virus ...

, and

Togaviridae {{Commonscat, Viruses by family This category is for articles about virus families (or redirects to such articles). There should be no subcategories. families Families (biology) ...

Data types in ViPR

Genomes A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

* Genome

annotations An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented in the margin of book pages. For anno ...

* Genes &

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

* Predicted protein domains and motifs * Immune

epitopes An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that binds to the epitope is called a paratope. Although ep ...

* Sequence Features * Orthologous protein clusters * 3D

protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ...

* 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 ( ingle-nucleotide polymorphismSNP): 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 Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...

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 (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

External links

* {{official website, http://www.viprbrc.org/, ViPR BRC
Bioinformatics Resource Centers
The NIAID page describing the goals and activities of the BRCs Biological databases Pathogen genomics