Comprehensive viral oligonucleotide probe design using conserved protein regions

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 challeng...

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Bibliographic Details
Published in:Nucleic Acids Research 2008-01, Vol.36 (1), p.e3-e3
Main Authors: Jabado, Omar J., Liu, Yang, Conlan, Sean, Quan, P. Lan, Hegyi, Hédi, Lussier, Yves, Briese, Thomas, Palacios, Gustavo, Lipkin, W. I.
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Conserved Sequence
Databases, Nucleic Acid
Databases, Protein
Genes, Viral
Genome, Viral
HIV-1 - genetics
Humans
Methods Online
Oligonucleotide Array Sequence Analysis
Oligonucleotide Probes - chemistry
Sequence Analysis, Protein - methods
Sequence Homology, Amino Acid
Viral Proteins - chemistry
Viral Proteins - genetics
Viruses - genetics
Viruses - isolation & purification
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkm1106