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Viral Bioinformatics Resource


NAR Molecular Biology Database Collection entry number 798
Upton C.1 and Lefkowitz E.J.2
1Department of Biochemistry and Microbiology, University of Victoria, Ring Road, PO Box 3055 STN CSC, Victoria, BC V8W 3P6, Canada
2Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA

Database Description

The Viral Bioinformatics Resource Center (VBRC) is one of eight NIH-sponsored Bioinformatics Resource Centers (http://www.brc-central.org/) established to provide informational and analytical resources to the scientific community. The goal of these Centers is to aid research directed at providing a better understanding of microorganisms included on the NIH list of priority pathogens. This list includes pathogens considered to be potential threats as agents of bioterrorism, as well as pathogens classified as causing emerging or re-emerging infectious diseases. The VBRC was specifically directed to study viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that supports the data storage, annotation, analysis, and information exchange goals of this work. The current release consists of 369 complete genomic sequences (v 4.2). In addition to sequence data, the VBRC provides curation for each of the viral genomes and the gene records, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype-with special emphasis on pathogenesis. To the extent possible, the curation will also include information on the involvement of genes in host-pathogen interactions. In addition to the sequence database, we will also be collecting, when available, data derived from high-throughput “Systems Biology” studies, including microarray gene expression data, proteomic analyses, and population genetics data. The VBRC also provides a variety of analytical tools on its web site to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. We are developing and making available visualization tools to provide a graphical display of the results of the various analyses. Finally, an important aspect of our ongoing work is to solicit feedback from the scientific community; the goal being to enhance and extend the VBRC, thereby increasing its use and usefulness in support of basic and applied research on these priority pathogens.

Recent Developments

Genome Annotation Transfer Utility (GATU), available from http://athena.bioc.uvic.ca, has been designed to facilitate quick and efficient annotation of viral genomes using a closely related annotated reference genome. It uses BLAST algorithms to look for and map ORFs from a reference sequence to target sequence, but also identifies ORFs unique to the new genome. A variety of graphical tools are provided to help the annotator verify predicted ORFs.

Longest common Substring Search (LCS) is a tool withing the Viral Genome Organiser (http://athena.bioc.uvic.ca), which finds the longest oligonucleotide common to a set of DNA sequences. It can also find multiple sequences longer than a given value.

Database of Virologists. The database interface allows users to register themselves and provide a variety of information, including affiliation, email address, www site, publications and viruses of interest. The datbase can be searched by virus or keywords. It is used to inform researchers of major changes to VBRC.

Acknowledgements

Ongoing funding of VBRC is provided by NIAID grant HHSN266200400036C.

References

1. Upton, C., D. Hogg, D. Perrin, M. Boone and N. Harris, 2001. Viral Genome Organizer: A system for analyzing complete viral genomes. Virus Research 70, 55-64.
2. Upton, C., Slack, S., Hunter, A.W., Ehlers, A. and R. L. Roper. 2003. Poxvirus Orthologous Clusters (POCs): Toward defining the minimum essential poxvirus genome. J. Virology, 77, 7590-7600.
3. Brodie, R., R. L. Roper, and C. Upton. 2004. JDotter: A Java Interface to Multiple DotPlots Generated by Dotter. Bioinformatics, 20, 279-281.
4. Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5:96.
5. Wang, C. and E. J. Lefkowitz. 2004. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters. BMC Bioinformatics. 5:171.
6. Wang, C. and E. J. Lefkowitz. 2005. Refinement of Genomic Sequence Multiple Alignments Using a Genetic Algorithm. BMC Bioinformatics 6:200.
7. Lefkowitz, E. J., Upton, C., Changayil, S. S., Buck, C., Traktman, P. and R. M. L. Buller. 2005. Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. Nucleic Acids Res 2005 33: D311-D316.
8. Whitney, J., Esteban, D. J. and C. Upton. 2005. Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches. BMC Bioinformatics. 6:23.
9. Esteban, D. J., Da Silva, M. and C. Upton. 2005. New Bioinformatics Tools for Viral Genome Analyses at Viral Bioinformatics Ð Canada. Pharmacogenomics 6, 271-280.

Subcategory: Viral genome databases

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