About: Multiplex primer prediction software for divergent targets

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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	Multiplex primer prediction software for divergent targets
Creator	Hara, Christine Gardner, Shea Colston, Bill Hiddessen, Amy Wagner, Mark Williams, Peter
Source	PMC
abstract	We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.
has issue date	2009-09-16(xsd:dateTime)
bibo:doi	10.1093/nar/gkp659
bibo:pmid	19759213
has license	cc-by-nc
sha1sum (hex)	36fd2f3dfeec8932ec6e4553bce33222c4380756
schema:url	https://doi.org/10.1093/nar/gkp659
resource representing a document's title	Multiplex primer prediction software for divergent targets
has PubMed Central identifier	PMC2770652
has PubMed identifier	19759213
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:36fd2f3dfeec8932ec6e4553bce33222c4380756#body_text
is schema:about of	named entity 'INFLUENZA A VIRUS' named entity 'NEURAMINIDASE' named entity 'ALGORITHM' named entity 'HEMAGGLUTININ' named entity 'CONSERVED' named entity 'SPECIFIC' named entity 'AVAILABLE' named entity 'NUMBER OF' named entity 'AMPLICON' named entity 'FAMILY' named entity 'PRIMER' named entity 'MULTIPLEX' named entity 'PREDICTION' named entity 'DOES NOT' named entity 'VACCINIA VIRUS' named entity 'COMPATIBLE' named entity 'HIV-1' named entity 'TARGETS' named entity 'PRIMER' named entity 'PRIMING' named entity 'AMPLIFY' named entity 'VIRUSES' named entity 'GENERATE' named entity 'MERS' named entity 'VIRAL DETECTION' named entity 'PREDICTION' named entity 'SOFTWARE' named entity 'POXVIRIDAE' named entity 'DESCRIBE' named entity 'TARGET' named entity 'DEMONSTRATED' named entity 'SOFTWARE' named entity 'PRIMERS' named entity 'MPP' named entity 'VIRAL' named entity 'BUILD' named entity 'SEGMENTS' named entity 'SEQUENCES' named entity 'SPECIES' named entity 'MULTIPLEX' named entity 'NORWALK VIRUS' named entity 'MEMBERS' named entity 'TO PRODUCE' named entity 'MULTIPLE SEQUENCE ALIGNMENT' named entity 'FOOT-AND-MOUTH DISEASE VIRUS' named entity 'LARGER' named entity 'APPLICATION' named entity 'APPLIED' named entity 'SET' named entity 'SHORT' named entity 'LARGE' named entity 'DIVERSE' covid:arg/36fd2f3dfeec8932ec6e4553bce33222c4380756 named entity 'algorithm' named entity 'primer' named entity 'sequenced' named entity 'viruses' named entity 'amplicons' named entity 'gene family' named entity 'genome' named entity 'human genome' named entity 'primers' named entity 'universal set' named entity 'amplicon sequencing' named entity 'nucleic acids' named entity 'highly conserved' named entity 'MSA' named entity 'degenerate primers' named entity 'vaccinia' named entity 'primers' named entity 'Hidden Markov Model' named entity 'inosine' named entity 'anneal' named entity 'TaqMan' named entity 'primers' named entity 'fingerprinting'

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