Comprehensive viral oligonucleotide probe design using conserved protein regions
Identifieur interne : 003834 ( Main/Exploration ); précédent : 003833; suivant : 003835Comprehensive viral oligonucleotide probe design using conserved protein regions
Auteurs : Omar J. Jabado [États-Unis] ; Yang Liu [États-Unis] ; Sean Conlan [États-Unis] ; P. Lan Quan [États-Unis] ; Hédi Hegyi [États-Unis] ; Yves Lussier [États-Unis] ; Thomas Briese [États-Unis] ; Gustavo Palacios [États-Unis] ; W. I. Lipkin [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2008.
Abstract
Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.
Url:
DOI: 10.1093/nar/gkm1106
Affiliations:
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I." last="Lipkin">W. I. Lipkin</name><affiliation wicri:level="4"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1801, New York, NY 10032, Sigma-Aldrich, Research Biotech, 2909 Laclede Ave, St. Louis, MO 63103, USA, Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, PO Box 7, Hungary and Center for Biomedical Informatics, Department of Medicine, Section of Genetic Medicine, University of Chicago, 5841 South Maryland Ave, AMB N660B, Chicago, IL 60637</wicri:regionArea><placeName><region type="state">Illinois</region><settlement type="city">New York</settlement></placeName><orgName type="university">Université Columbia</orgName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published">2008</date><date type="e-published">2007</date><biblScope unit="vol">36</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="e3">e3</biblScope><biblScope unit="page" to="e3">e3</biblScope></imprint><idno type="ISSN">0305-1048</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Illinois</li></region><settlement><li>New York</li></settlement><orgName><li>Université Columbia</li></orgName></list><tree><country name="États-Unis"><region name="Illinois"><name sortKey="Jabado, Omar J" sort="Jabado, Omar J" uniqKey="Jabado O" first="Omar J." last="Jabado">Omar J. Jabado</name></region><name sortKey="Briese, Thomas" sort="Briese, Thomas" uniqKey="Briese T" first="Thomas" last="Briese">Thomas Briese</name><name sortKey="Conlan, Sean" sort="Conlan, Sean" uniqKey="Conlan S" first="Sean" last="Conlan">Sean Conlan</name><name sortKey="Hegyi, Hedi" sort="Hegyi, Hedi" uniqKey="Hegyi H" first="Hédi" last="Hegyi">Hédi Hegyi</name><name sortKey="Lipkin, W I" sort="Lipkin, W I" uniqKey="Lipkin W" first="W. I." last="Lipkin">W. I. Lipkin</name><name sortKey="Lipkin, W I" sort="Lipkin, W I" uniqKey="Lipkin W" first="W. I." last="Lipkin">W. I. Lipkin</name><name sortKey="Lipkin, W I" sort="Lipkin, W I" uniqKey="Lipkin W" first="W. I." last="Lipkin">W. I. Lipkin</name><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><name sortKey="Lussier, Yves" sort="Lussier, Yves" uniqKey="Lussier Y" first="Yves" last="Lussier">Yves Lussier</name><name sortKey="Palacios, Gustavo" sort="Palacios, Gustavo" uniqKey="Palacios G" first="Gustavo" last="Palacios">Gustavo Palacios</name><name sortKey="Quan, P Lan" sort="Quan, P Lan" uniqKey="Quan P" first="P. Lan" last="Quan">P. Lan Quan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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