Comprehensive viral oligonucleotide probe design using conserved protein regions

Omar J. Jabado, Yang Liu, Sean Conlan, P. Lan Quan, Hédi Hegyi, Yves Lussier, Thomas Briese, Gustavo Palacios, W. I. Lipkin

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

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.

Original languageEnglish (US)
Article numbere3
JournalNucleic acids research
Volume36
Issue number1
DOIs
StatePublished - Jan 2008
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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