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Viral Bioinformatics Resource Center
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<h2 id="virus-families-covered-in-the-vbrc-database">Virus families covered in the VBRC database</h2> <p>The VBRC covers the following viruses: </p> <ul><li><a href="/facts/Poxviridae/L2oTmrnq">Poxviridae</a></li> <li><a href="/facts/Asfarviridae/rDt0Gh75">Asfarviridae</a></li></ul> <h2 id="organization-of-the-vbrc-database">Organization of the VBRC database</h2> <p>The VBRC database stores viral bioinformatic data on three levels: </p> <ol><li>Whole genomes. This level contains information about the virus species or isolate and its entire genomic sequence.</li> <li>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.</li> <li>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.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> 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."<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a>[<i>self-published source?</i>]</li></ol> <h2 id="central-tools-provided-by-vbrc">Central Tools Provided by VBRC</h2> <p>VBRC provides researchers with a wide variety of database-linked tools. Of these, the central four programs are VOCs, VGO, BBB, and JDotter. </p> <ol><li>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.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a></li> <li>VGO (Viral Genome Organizer) VGO is a Java-based interface used for viewing and searching viral genome sequences.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> 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.</li> <li>BBB (Base-by-Base) Base-By-Base is a platform-independent (Java-based), whole-genome pairwise and multiple alignment editor.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> 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.</li> <li>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 <a href="/facts/Dot_plot_(bioinformatics)/7zhgPAGd">dotplots</a>. JDotter also interfaces with the curated database or the user-supplied file to display supplementary feature data such as gene annotations.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a></li></ol> <h2 id="other-tools-provided-by-vbrc">Other Tools Provided by VBRC</h2> <p>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. <a href="/facts/Regular_expression/KFL3veHX">regular expression</a> 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. </p><p>These additional tools are as follows: </p> <ul><li>Sequence Searcher performs regular expression and fuzzy motif searches of DNA or protein sequences, and is built into VOCS.</li> <li>GFS (Genome Fingerprint Scanning) maps peptide mass fingerprint data to genomic sequences. It is built into VOCS.</li> <li>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.</li> <li>GraphDNA provides DNA skews and walks (a <a href="/facts/Cartesian_plane/lkTqvMmB">Cartesian plane</a>-based representation of nucleotide content) from a VBRC database- or user-supplied DNA sequence. It is integrated into VOCS.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a></li> <li>Hydrophobicity Plotter generates a <a href="/facts/Hydrophobicity/Ifya0CXQ">hydrophobicity</a> graph for a VBRC database- or user-supplied protein sequence. Three hydrophobicity scales (<a href="/facts/Kyte-Doolittle_scale/6TkSVjjy">Kyte-Doolittle</a>, 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.</li> <li>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.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></li></ul> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Bioinformatics_Resource_Centers/hQAFSQ7A">Bioinformatics Resource Centers</a></li> <li><a href="/facts/National_Institute_of_Allergy_and_Infectious_Diseases/PD8bQnvS">National Institute of Allergy and Infectious Diseases</a></li> <li><a href="/facts/Bioinformatics/D5x2L8ee">Bioinformatics</a></li></ul> <h2 id="further-reading">Further reading</h2> <ul><li><i>Bioinformatics for Analysis of Poxvirus Genomes</i> <a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></li> <li><i>It's a small world after all — viral genomics and the global dominance of viruses</i> <a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a></li> <li><i>Bioinformatic Approaches for Comparative Analysis of Viruses</i> <a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://4virology.net">[1]</a> Viral Bioinformatics Resource Center Analytical Workbench (contains Java-based tools)</li> <li><a href="http://www.niaid.nih.gov">NIAID home page</a></li> <li><a href="https://web.archive.org/web/20090420082012/http://www3.niaid.nih.gov/research/resources/brc/default.htm">Bioinformatics Resource Centers</a> The NIAID page describing the goals and activities of the BRCs</li> <li><a href="https://web.archive.org/web/20110105165721/http://pathogenportal.org/">Pathogen Portal</a> Hub site for the BRCs; provides summary information</li> <li><a href="https://4virology.net/virology-ca-tools/vocs/">[2]</a> Virus Orthologous Clusters launch page</li> <li><a href="https://4virology.net/virology-ca-tools/vgo/">[3]</a> Viral Genome Organizer launch page</li> <li><a href="https://4virology.net/virology-ca-tools/base-by-base/">[4]</a> Base-by-Base launch page</li> <li><a href="https://4virology.net/virology-ca-tools/jdotter/">[5]</a> JDotter launch page</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"VBRC". Viral Bioinformatics Resource Center. Dr. Chris Upton. <a href="https://4virology.net/" target="_blank">https://4virology.net/</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Upton, Chris. "Professor of Biochemistry and Microbiology". <a href="https://scholar.google.ca/citations?user=Xu2GmhAAAAAJ&hl=en" target="_blank">https://scholar.google.ca/citations?user=Xu2GmhAAAAAJ&hl=en</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Upton, C.; Slack, S; Hunter, AL; Ehlers, A; Roper, RL (Jul 2003). "Poxvirus Orthologous Clusters: toward Defining the Minimum Essential Poxvirus Genome". Journal of Virology. 77 (13): 7590–600. doi:10.1128/JVI.77.13.7590-7600.2003. ISSN 0022-538X. PMC 164831. PMID 12805459. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC164831" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC164831</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Upton, Chris (4 July 2008). "Bioinformatics Tools and their Applications in Virology". Retrieved 4 September 2009. <a href="http://topics.scirus.com/Bioinformatics_Tools_and_Their_Applications_in_Virology.html" target="_blank">http://topics.scirus.com/Bioinformatics_Tools_and_Their_Applications_in_Virology.html</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Ehlers, A.; Osborne, J.; Slack, S.; Roper, R. L.; Upton, C. (2002). "Poxvirus Orthologous Clusters (POCs)". Bioinformatics. 18 (11): 1544–5. doi:10.1093/bioinformatics/18.11.1544. PMID 12424130. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Upton, C; Hogg, D; Perrin, D; Boone, M; Harris, NL (Sep 2000). "Viral genome organizer: a system for analyzing complete viral genomes". Virus Research. 70 (1–2): 55–64. doi:10.1016/S0168-1702(00)00210-0. ISSN 0168-1702. PMID 11074125. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Brodie, Ryan; Smith, AJ; Roper, RL; Tcherepanov, V; Upton, C (Jul 2004). "Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments". BMC Bioinformatics. 5: 96. doi:10.1186/1471-2105-5-96. PMC 481056. PMID 15253776. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC481056" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC481056</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Shin-Lin Tu; Jeannette P. Staheli; Colum McClay; Kathleen McLeod; Timothy M. Rose; Chris Upton (2018). "Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes". Viruses. 10 (11): 637. doi:10.3390/v10110637. PMC 6265842. PMID 30445717. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265842" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265842</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Hillary, William; Lin, Song-Han; Upton, Chris (2011). "Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments". Microbial Informatics and Experimentation. 1 (1): 2. doi:10.1186/2042-5783-1-2. PMC 3348662. PMID 22587754. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348662" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348662</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Brodie, R.; Roper, RL; Upton, C (Jan 2004). "JDotter: a Java interface to multiple dotplots generated by dotter". Bioinformatics. 20 (2): 279–81. doi:10.1093/bioinformatics/btg406. ISSN 1367-4803. PMID 14734323. <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtg406" target="_blank">https://doi.org/10.1093%2Fbioinformatics%2Fbtg406</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Thomas, Jamie M; Horspool, D; Brown, G; Tcherepanov, V; Upton, C (Jan 2007). "GraphDNA: a Java program for graphical display of DNA composition analyses". BMC Bioinformatics. 8: 21. doi:10.1186/1471-2105-8-21. PMC 1783863. PMID 17244370. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1783863" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1783863</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Tcherepanov, Vasily; Ehlers, A; Upton, C (Jun 2006). "Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome". BMC Genomics. 7: 150. doi:10.1186/1471-2164-7-150. PMC 1534038. PMID 16772042. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534038" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534038</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Da Silva, Melissa; Upton, Chris (2012). Vaccinia Virus and Poxvirology. Methods in Molecular Biology. Vol. 890. Melissa Da Silva and Chris Upton. pp. 233–258. doi:10.1007/978-1-61779-876-4_14. ISBN 978-1-61779-875-7. PMID 22688771. <a href="978-1-61779-875-7" target="_blank">978-1-61779-875-7</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Ghedin, Elodie; Upton, Chris (2011). "It's a small world after all — viral genomics and the global dominance of viruses". Current Opinion in Virology. 1 (4): 280–281. doi:10.1016/j.coviro.2011.08.001. PMID 22440784. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Amgarten, Deyvid; Upton, Chris (2018). Comparative Genomics. Methods in Molecular Biology. Vol. 1704. Deyvid Amgarten and Chris Upton. pp. 401–417. doi:10.1007/978-1-4939-7463-4_15. ISBN 978-1-4939-7461-0. PMID 29277875. <a href="978-1-4939-7461-0" target="_blank">978-1-4939-7461-0</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> </ol>