About: Comprehensive viral oligonucleotide probe design using conserved protein regions

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Comprehensive viral oligonucleotide probe design using conserved protein regions
Creator	Liu, Yang Palacios, Gustavo Briese, Thomas Conlan, Sean Lussier, Yves Jabado, Omar Lipkin, W Di Hegyi, Hé Quan, P
Source	Medline; PMC
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.
has issue date	2007-12-13(xsd:dateTime)
bibo:doi	10.1093/nar/gkm1106
bibo:pmid	18079152
has license	cc-by-nc
sha1sum (hex)	ad7e256a901378cfdb314e11ab3504eda659df42
schema:url	https://doi.org/10.1093/nar/gkm1106
resource representing a document's title	Comprehensive viral oligonucleotide probe design using conserved protein regions
has PubMed Central identifier	PMC2248741
has PubMed identifier	18079152
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:ad7e256a901378cfdb314e11ab3504eda659df42#body_text
is schema:about of	named entity 'PROTEIN ' named entity 'FINDING' named entity 'OLIGONUCLEOTIDE PROBES' named entity 'HAVE' named entity 'VIROLOGY' named entity 'GENETIC' named entity 'CHALLENGE' named entity 'STATIC' named entity 'WIDE' named entity 'DESIGN' named entity 'DATABASE' named entity 'AMINO ACID' named entity 'DISCOVERY' named entity 'COMPREHENSIVE' named entity 'WHERE' named entity 'VIRUS DETECTION' named entity 'NEAR COMPLETE' named entity 'TESTING' named entity 'PROBE DESIGN' named entity 'RAPID' named entity 'ADDRESS' named entity 'COMPREHENSIVE' named entity 'TO INCREASE' named entity 'HERE' named entity 'IN SILICO' named entity 'PROBE' named entity 'RANGE' named entity 'MOTIF' named entity 'PROBE DESIGN' named entity 'REGIONS' named entity 'VIRAL' named entity 'USING' named entity 'VIRAL SEQUENCE' named entity 'DERIVED' named entity 'APPLIED' named entity 'DENSITY' named entity 'TARGETS' named entity 'REGIONS' named entity 'REQUIRED' named entity 'EXPANSION' named entity 'OLIGONUCLEOTIDE PROBE' named entity 'HIGHLY' named entity 'PROTEIN FAMILIES DATABASE' named entity 'PRESENT' named entity 'BASED' named entity 'USING' named entity 'THERMODYNAMIC MODEL' named entity 'PROTEIN SEQUENCES' named entity 'SEQUENCES' named entity 'CONSERVED' named entity 'PROBLEMS' named entity 'SEQUENCE DATABASE' named entity 'SOLUTIONS' named entity 'MICROBIAL' named entity 'UNIQUE' named entity 'METHOD' named entity 'STRATEGY' named entity 'SEQUENCE' named entity 'INDICATED' named entity 'RESPONSIVE TO' named entity 'PRINTING' named entity 'USES' named entity 'CONSERVED' named entity 'ALGORITHMS' named entity 'COVERAGE' named entity 'EVOLUTION' named entity 'MICROBIAL SURVEILLANCE' named entity 'TO IDENTIFY' named entity 'OLIGONUCLEOTIDE MICROARRAYS' named entity 'thermodynamic' named entity 'multiplexed' named entity 'motif' named entity 'sequence database'

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