About: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

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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 Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
Creator	Elsheikh, Maher Peña, José Jaing, Crystal Gardner, Shea Borucki, Monica Hysom, David
Source	Medline; PMC
abstract	Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.
has issue date	2014-08-03(xsd:dateTime)
bibo:doi	10.1155/2014/101894
bibo:pmid	25157264
has license	cc-by
sha1sum (hex)	692fedb674101b505fb28fe7b96e552ed224c07d
schema:url	https://doi.org/10.1155/2014/101894
resource representing a document's title	Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
has PubMed Central identifier	PMC4137498
has PubMed identifier	25157264
schema:publication	Adv Bioinformatics
resource representing a document's body	covid:692fedb674101b505fb28fe7b96e552ed224c07d#body_text
is schema:about of	named entity 'TARGETED' named entity 'PRIMER DESIGN' named entity 'DEGENERATE' named entity 'VIRAL' named entity 'GENOMES' named entity 'MULTIPLEX' named entity 'WHOLE GENOME AMPLIFICATION' named entity 'Amplification' named entity 'primers' named entity 'genome sequencing' named entity 'entire genomes' named entity 'primers' named entity 'CalTech' named entity 'multiplex PCR' named entity 'primers' named entity 'RNA' named entity 'NCBI' named entity 'primer dimers' named entity 'Life Technologies' named entity 'amplicons' named entity 'primers' named entity 'Invitrogen' named entity 'amplicons' named entity 'Manassas' named entity 'mice' named entity 'primers' named entity 'gene family' named entity 'clade' named entity 'phylogeny' named entity 'genomes' named entity 'PCR' named entity 'amplicons' named entity 'virus' named entity 'primer dimer' named entity 'primers' named entity 'PCR primer design' named entity 'amplicons' named entity 'cDNA' named entity 'primers' named entity 'anneal' named entity 'genome' named entity 'maize' named entity 'Nsp3' named entity 'genome' named entity 'PCR primer design' named entity 'Low complexity regions' named entity 'amplicons' named entity 'degenerate primers' named entity 'primers' named entity 'PCR' named entity 'primers' named entity 'viral genomes' named entity 'primers' named entity 'Richard Bowen' named entity 'amplicons' named entity 'primers' named entity 'MSA' named entity 'PCR primer design' named entity 'genome' named entity 'primers' named entity 'murine' named entity 'viruses' named entity 'PCR' named entity 'virus' named entity 'primers' named entity 'primers' named entity 'clade' named entity 'cDNA' named entity 'sequence variation' named entity 'free energy' named entity 'amplicons' named entity 'high throughput sequencing' named entity 'JCVI' named entity 'amplicons' named entity 'amplicon' named entity 'primers'

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