ArticleNucleic acids research2008
Comprehensive viral oligonucleotide probe design using conserved protein regions.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Context-dependent effects of antimicrobial coatings on microbial load and bacterial community composition on public high-touch surfaces.Microbiome · 2026Article
- Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.Nature biotechnology · 2019Article
- In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment.BMC medical genomics · 2014Article
- Detection of dengue group viruses by fluorescence in situ hybridization.Parasites & vectors · 2012Article
- Article
- A microbial detection array (MDA) for viral and bacterial detection.BMC genomics · 2010Article
- Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models.BMC bioinformatics · 2010Article
- Nonparametric methods for the analysis of single-color pathogen microarrays.BMC bioinformatics · 2010Article
- Z proteins of New World arenaviruses bind RIG-I and interfere with type I interferon induction.Journal of virology · 2010Article
- Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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.
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Registered trials
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