The Viral Bioinformatics Resource Center (VBRC) is an online resource providing access to a

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases s ...

of curated viral

genomes In the fields of molecular biology and genetics, 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 g ...

and a variety of tools for

bioinformatic Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...

genome analysis. This resource was one of eight BRCs (

Bioinformatics Resource Centers The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID (the National Institute of Allergy and Infectious Diseases.)NIAID 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 (HHS). NIAID' ...

with the goal of promoting research against emerging and re-emerging

pathogens In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a ger ...

, particularly those seen as potential

bioterrorism Bioterrorism is terrorism involving the intentional release or dissemination of biological agents. These agents are bacteria, viruses, insects, fungi, and/or toxins, and may be in a naturally occurring or a human-modified form, in much the same ...

threats. The VBRC is now supported by Dr. Chris Upton at the

University of Victoria The University of Victoria (UVic or Victoria) is a public research university located in the municipalities of Oak Bay and Saanich, British Columbia, Canada. The university traces its roots to Victoria College, the first post-secondary insti ...

. The curated VBRC database contains all publicly available genomic sequences for poxviruses and African Swine Fever Viruses (ASFV). A unique aspect of this resource relative to other genomic databases is its grouping of all

annotated 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 ann ...

genes into ortholog groups (i.e. protein families) based on pre-run BLASTP sequence similarity searches. The curated database is accessed through VOCS (Viral Orthologous Clusters), a downloadable

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...

-based user interface, and acts as the central information source for other programs of the VBRC workbench. These programs serve a variety of bioinformatic analysis functions (whole- or subgenome alignments, genome display, and several types of gene/protein sequence analysis). The majority of these tools are programmed to take user-supplied input as well.

Virus families covered in the VBRC database

The VBRC covers the following viruses: *

Poxviridae ''Poxviridae'' is a family of double-stranded DNA viruses. Vertebrates and arthropods serve as natural hosts. There are currently 83 species in this family, divided among 22 genera, which are divided into two subfamilies. Diseases associated wit ...

* Asfarviridae

Organization of the VBRC database

The VBRC database stores viral bioinformatic data on three levels: # Whole genomes. This level contains information about the virus species or isolate and its entire genomic sequence. # Annotated genes. This level contains all the predicted ORFs (open reading frames) in a particular virus genome, together with their DNA and (translated) protein sequences. # Ortholog groups (families). This level is a distinguishing feature of the VBRC database. Each annotated gene, after it has been entered into the database, is subjected to BLASTP searching against all other genes already in the database. Based on the search results, it is either assigned to a pre-existing ortholog group or placed in a newly created ortholog group of its own. The goal of this level is to "allow for quick comparison of similar genes across a given virus family."

Central Tools Provided by VBRC

VBRC provides researchers with a wide variety of database-linked tools. Of these, the central four programs are VOCs, VGO, BBB, and JDotter. # VOCs (Viral Orthologous Clusters)
VOCs is the main database access interface. Users can search the available data by a number of criteria related to genome, gene, or ortholog group characteristics. Search results are displayed in table format; from here the user may obtain further information about a particular database entry, or launch a VOCs-linked tool (see below) for analysis of selected data. Additional analysis tools such as BLAST searches, genome maps, genome or gene alignment, phylogenetic trees, etc. are provided. # VGO (Viral Genome Organizer)
VGO is a Java-based interface used for viewing and searching viral genome sequences. Together with a graphical representation of the selected VBRC (or user-supplied) genome, the program displays information relevant to a genome of interest, including its genes, ORFs and start/stop codons. Tools are provided allowing the user to perform regular expression, a fuzzy motif, and masslist searches. VGO can also be used to identify related genes across multiple sequences. # BBB (Base-by-Base)
Base-By-Base is a platform-independent (Java-based), whole-genome pairwise and multiple alignment editor. The program highlights differences between consecutive pairs of sequences within an alignment, thus allowing the user to survey a large alignment at a single-residue level. Annotations from the VBRC database or user-supplied files are displayed alongside each sequence.
Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it also generates multiple alignments using Clustal Omega, T-Coffee and MUSCLE. Edit functions are provided to allow users to fine-tune such alignments manually; users may also annotate genomes with comments or primer sequences. # JDotter
JDotter is a Java-based user interface providing VBRC-linked access to the Linux version of Dotter. JDotter can both access pre-processed dotplots of the genome and gene (DNA or protein) sequences available in the VBRC database, and take user input for generation of new dotplots. JDotter also interfaces with the curated database or the user-supplied file to display supplementary feature data such as gene annotations.

Other Tools Provided by VBRC

VBRC provides a number of additional Java-based analysis tools on its website. The tools in this category are each designed to perform a very specific task (e.g.

regular expression A regular expression (shortened as regex or regexp; sometimes referred to as rational expression) is a sequence of characters that specifies a search pattern in text. Usually such patterns are used by string-searching algorithms for "find" ...

searches, DNA skew plotting) and, though they can be accessed as stand-alone programs with user-supplied input, most have increased utility when launched from the central VOCS application with VBRC-supplied data. These additional tools are as follows: * Sequence Searcher performs regular expression and fuzzy motif searches of DNA or protein sequences, and is built into VOCS. * GFS (Genome Fingerprint Scanning) maps peptide mass fingerprint data to genomic sequences. It is built into VOCS. * NAP (Nucleotide Amino Acid Alignment) is a Java interface to napC, a program designed to align a nucleotide and protein sequence, taking terminal gaps and insertion/deletion mutations into account. It can be accessed from VOCS. * GraphDNA provides DNA skews and walks (a

Cartesian plane A Cartesian coordinate system (, ) in a plane is a coordinate system that specifies each point uniquely by a pair of numerical coordinates, which are the signed distances to the point from two fixed perpendicular oriented lines, measured in ...

-based representation of nucleotide content) from a VBRC database- or user-supplied DNA sequence. It is integrated into VOCS. * Hydrophobicity Plotter generates a

hydrophobicity In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, t ...

graph for a VBRC database- or user-supplied protein sequence. Three hydrophobicity scales ( Kyte-Doolittle, Hopp-Woods, and Parker-Guo-Hodges) are supported; the graphing procedure is based on a sliding window of user-determined length. It can be accessed from VOCS. * GATU (Genome Annotation Transfer Utility) allows a user to annotate a newly sequenced genome based on the annotations present in a reference genome; it can also predict new genes in the query genome.

References

External links

Viral Bioinformatics Resource Center Analytical Workbench (contains Java-based tools)
NIAID home page

The NIAID page describing the goals and activities of the BRCs
Pathogen Portal
Hub site for the BRCs; provides summary information

Virus Orthologous Clusters launch page

Viral Genome Organizer launch page

Base-by-Base launch page

JDotter launch page Biological databases Bioinformatics software