About: Design of a set of probes with high potential for influenza virus epidemiological surveillance

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About: Design of a set of probes with high potential for influenza virus epidemiological surveillance Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Design of a set of probes with high potential for influenza virus epidemiological surveillance
Creator	Jaimes-Díaz, Hueman Larios-Serrato, V Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso Pérez-Cervantes, Hilda Zepeda-López, Héctor Carreño-Durán, Luis Javier Sánchez-Vallejo, Carlos Olguín-Ruiz, Gabriela
Source	Medline; PMC
abstract	An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences with Tm values between 34.5 and 36.5oC were applied for selecting probes with high sequential entropy. Virtual Hybridization was used to predict Genomic Fingerprints to assess the capability of the IPS to discriminate between influenza and related strains. Distance scores between pairs of Influenza Genomic Fingerprints were calculated, and used for estimating Taxonomic Trees. Visual examination of both Genomic Fingerprints and Taxonomic Trees suggest that the IPS is able to discriminate between distant and closely related Influenza strains. It is proposed that the IPS can be used to investigate, by virtual or experimental hybridization, any new, and potentially virulent, strain.
has issue date	2013-04-30(xsd:dateTime)
bibo:doi	10.6026/97320630009414
bibo:pmid	23750091
has license	no-cc
sha1sum (hex)	4b7bfd89ad2142ae4d193ed7925dc02889e31c27
schema:url	https://doi.org/10.6026/97320630009414
resource representing a document's title	Design of a set of probes with high potential for influenza virus epidemiological surveillance
has PubMed Central identifier	PMC3670124
has PubMed identifier	23750091
schema:publication	Bioinformation
resource representing a document's body	covid:4b7bfd89ad2142ae4d193ed7925dc02889e31c27#body_text
is schema:about of	named entity 'Fingerprints' named entity 'IPS' named entity 'experimental' named entity 'probes' named entity 'strains' named entity 'ABLE TO' named entity 'SURVEILLANCE' named entity 'MER' named entity 'DISTANTLY' named entity 'RELATED' named entity 'SEGMENTS' named entity 'TRIMER' named entity 'APPLIED' named entity 'SEARCHED' named entity 'TREES' named entity 'GENOMIC' named entity 'MINIMUM' named entity 'IN SILICO' named entity 'SEQUENTIAL' named entity 'REPEATS' named entity 'SITES' named entity 'HYBRIDIZATION' named entity 'STRAIN' named entity 'DIVERSE' named entity 'ADDITIONAL' named entity 'IPS' named entity 'CONSECUTIVE' named entity 'DERIVED' named entity 'DIMER' named entity 'TO INVESTIGATE' named entity 'ALIGNED' covid:arg/4b7bfd89ad2142ae4d193ed7925dc02889e31c27 named entity 'SET' named entity 'SET' named entity 'PROBES' named entity 'ASSESS' named entity 'GENOMES' named entity 'ALIGNMENT' named entity 'RNA' named entity 'CONTENT' named entity 'CRITERIA' named entity 'SCORES' named entity 'TESTED' named entity 'SELECTING' named entity 'ABSENCE OF' named entity 'PREDICT' named entity 'SUGGEST' named entity 'PROBES' named entity 'PROPOSED' named entity 'INFLUENZA VIRUS' named entity 'EPIDEMIOLOGICAL' named entity 'HIGH' named entity 'DESIGN' named entity 'HYPOTHESIS' named entity 'NEW' named entity 'DISCRIMINATE' named entity 'FINGERPRINTING' named entity 'ESTIMATING' named entity 'PAIRS' named entity 'EXPERIMENTAL' named entity 'FINGERPRINTS' named entity 'STRAINS' named entity 'DISTANCE' named entity 'VALUES' named entity 'DISTANT' named entity 'CAPABILITY' named entity 'POTENTIAL' named entity 'SEQUENCES' named entity 'CALCULATED' named entity 'USED' named entity 'VISUAL EXAMINATION' named entity 'HIGH' named entity 'PROBE'

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