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

National Institute of Allergy and Infectious Diseases

The National Institute of Allergy and Infectious Diseases is one of the 27 institutes and centers that make up the National Institutes of Health , an agency of the United States Department of Health and Human Services...

 (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

Bioinformatics Resource Centers

The Bioinformatics Resource Centers are a group of five Internet-based research centers established in 2004 and funded by NIAID The BRCs were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in...

 (BRC) funded by NIAID, a component of the National Institutes of Health

National Institutes of Health

The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 (NIH), which is an agency of the United States Department of Health and Human Services

United States Department of Health and Human Services

The United States Department of Health and Human Services is a Cabinet department of the United States government with the goal of protecting the health of all Americans and providing essential human services. Its motto is "Improving the health, safety, and well-being of America"...

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Virus families covered in ViPR

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

Bunyaviridae

Bunyaviridae is a family of negative-stranded RNA viruses. Though generally found in arthropods or rodents, certain viruses in this family occasionally infect humans. Some of them also infect plants....

, Caliciviridae

Caliciviridae

The Caliciviridae family are a family of viruses, members of Class IV of the Baltimore scheme. They are positive-sense, single stranded RNA which is non-segmented. The caliciviruses have been found in a number of organisms such as humans, cattle, pigs, cats, chickens, reptiles, dolphins and...

, Coronaviridae

Coronaviridae

Coronaviruses are enveloped, single-stranded, positive-sense RNA viruses with club-shaped surface about 120-160 nm in diameter that resemble a “corona”.-Virology:...

, Filoviridae

Filoviridae

The family Filoviridae is the taxonomic home of several related viruses that form filamentous virions. Two members of the family that are commonly known are Ebola virus and Marburg virus. Both viruses, and some of their lesser known relatives, cause severe disease in humans and nonhuman primates in...

, Flaviviridae

Flaviviridae

The Flaviviridae are a family of viruses that are primarily spread through arthropod vectors . The family gets its name from Yellow Fever virus, a type virus of Flaviviridae; flavus means yellow in Latin...

, Hepeviridae, Herpesviridae

Herpesviridae

The Herpesviridae are a large family of DNA viruses that cause diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word herpein , referring to the latent, recurring infections typical of this group of viruses...

, Paramyxoviridae, Picornaviridae, Poxviridae

Poxviridae

Poxviruses are viruses that can, as a family, infect both vertebrate and invertebrate animals.Four genera of poxviruses may infect humans: orthopox, parapox, yatapox, molluscipox....

, Reoviridae

Reoviridae

Reoviridae is a family of viruses that can affect the gastrointestinal system and respiratory tract. Viruses in the family Reoviridae have genomes consisting of segmented, double-stranded RNA...

, Rhabdoviridae

Rhabdoviridae

Rhabdoviruses are viruses belonging to the family Rhabdoviridae, which is in the order Mononegavirales. The name is derived from the Greek rhabdos meaning rod referring to the shape of the viral particles. Rhabdoviruses infect a broad range of hosts throughout the animal and plant kingdoms...

, and Togaviridae

Togaviridae

The Togaviridae are a family of viruses, including the following genera:* Genus Alphavirus; type species: Sindbis virus, Eastern equine encephalitis virus, Western equine encephalitis virus, Venezuelan equine encephalitis virus, Ross River virus, O'nyong'nyong virus, Chikungunya* Genus Rubivirus;...

Data types in ViPR

• Genomes
• Genome annotations
• Genes & proteins
• Immune epitopes
• Sequence Features
• 3D protein structure
  Protein structure
  Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
  
  
• Clinical and surveillance data
• Computationally-derived data
• Host-pathogen interactions (coming soon)

Analysis and visualization tools in ViPR

• BLAST sequence similarity search
• Multiple sequence alignment
  Multiple sequence alignment
  A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
  
  
• Phylogenetic tree
  Phylogenetic tree
  A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
  
   construction
• 3D protein structures with Sequence Feature or epitope highlights
• Sequence Feature Variant Type
  Sequence feature variant type
  The Sequence Feature Variant Type refers to the defined mutation of a given sequence feature in a protein. Consider a protein, its amino acid sequence determines the its structure and function...
  
   (SFVT) analysis
• Metadata-driven comparative analysis
• Single-nucleotide polymorphism (SNP) analysis
• Genome annotation
• Personal Workbench to save and share data and analysis

External links

• Bioinformatics Resource Centers The NIAID page describing the goals and activities of the BRCs