biology

Viral Bioinformatics Resource Center

Viral Bioinformatics Resource Center is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Viral Bioinformatics Resource Center rather than just read about it. In short: The Viral Bioinformatics Resource Center (VBRC) is an online resource providing access to a database of curated viral genomes and a variety of tools for bioinformatic genome analysis. This resource was one of eight BRCs (Bioinformatics Resource Centers) funded by NIAID with the goal of promoting research against emerging and re-emerging pathogens, particularly those seen as potential bioterrorism threats.

Key takeaways

Viral Bioinformatics Resource Center belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Viral Bioinformatics Resource Center to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Viral Bioinformatics Resource Center from memory before moving on to harder problems.

Reference excerpt

The Viral Bioinformatics Resource Center (VBRC) is an online resource providing access to a database of curated viral genomes and a variety of tools for bioinformatic genome analysis. This resource was one of eight BRCs (Bioinformatics Resource Centers) funded by NIAID with the goal of promoting research against emerging and re-emerging pathogens, particularly those seen as potential bioterrorism threats. The VBRC is now supported by Dr. Chris Upton at the University of Victoria. 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 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-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 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 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-based representation of nucleotide content) from a VBRC database- or user-supplied DNA sequence. It is integrated into VOCS. Hydrophobicity Plotter generates a hydrophobicity 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.

See also Bioinformatics Resource Centers National Institute of Allergy and Infectious Diseases Bioinformatics

References

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Worked examples

Example 1 — a first encounter with Viral Bioinformatics Resource Center

Start with the simplest possible case. Write down what Viral Bioinformatics Resource Center claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Viral Bioinformatics Resource Center before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Viral Bioinformatics Resource Center ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Viral Bioinformatics Resource Center

In research: Viral Bioinformatics Resource Center appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Viral Bioinformatics Resource Center in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Viral Bioinformatics Resource Center is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics software, Biological databases, so understanding it makes those chapters shorter.
In everyday life: Look for Viral Bioinformatics Resource Center outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Viral Bioinformatics Resource Center in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Viral Bioinformatics Resource Center means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Viral Bioinformatics Resource Center out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Viral Bioinformatics Resource Center in simple terms?

Why does Viral Bioinformatics Resource Center matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Viral Bioinformatics Resource Center?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Viral Bioinformatics Resource Center.