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VirOligo


NAR Molecular Biology Database Collection entry number 303
Onodera K., Song Y. and Melcher U.
Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74074, USA

Database Description

VirOligo is a database of virus-specific oligonucleotides. VirOligo contains PCR primers and hybridization probes used for detection of viral nucleic acids and the experimental conditions used in their detection. The latter include temperature regimes, concentrations of reagent components, and enzymes used. Each entry contains links to PubMed, GenBank, NCBI Taxonomy databases and BLAST. The organization of the relational database includes tables for the sources of the information, common reaction conditions, target of detection and the oligonucleotides.

Recent Developments

The VirOligo database continues to be expanded: as of October 2004, it contained almost 18,000 oligonucleotide entries and 4,700 experimental conditions derived from 3,658 journal articles that were published in English in peer-reviewed journals. The database structure, transparent to the user, has been revised substantially during the past year. The web interface has added the ability to initiate searches based on taxonomy ID, GI number or a precompiled list of viruses. Near complete coverage of approximately 30 viruses is available. These viruses or virus groups include bovine respiratory disease viruses, foot-and-mouth disease virus, variola (small pox) virus, cowpox virus, bovine parainfluenza virus, human adenovirus, influenza virus, vaccinia virus, canine parvovirus, porcine parvovirus, rodent parvovirus, tobamoviruses, potyviruses, SARS, borna virus, flaviviruses and arenaviruses. Combining these viruses with viruses whose coverage is incomplete, the VirOligo database contains information for more than 100 viruses. VirOligo data can be accessed additionally from NCBI PubMed, GenBank, and Taxonomy pages via LinkOut links and is linked from PathPort.

Acknowledgements

Samuel Roberts Noble Foundation, Ardmore, OK; IBIS Therapeutics; R. J. Sirny Professorship; Oklahoma Agricultural Experiment Station.


Go to the abstract in the NAR 2002 Database Issue.
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