Cargando…

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

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 de...

Descripción completa

Detalles Bibliográficos
Autores principales: Carreño-Durán, Luis R, Larios-Serrato, V, Jaimes-Díaz, Hueman, Pérez-Cervantes, Hilda, Zepeda-López, Héctor, Sánchez-Vallejo, Carlos Javier, Olguín-Ruiz, Gabriela Edith, Maldonado-Rodríguez, Rogelio, Méndez-Tenorio, Alfonso
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670124/
https://www.ncbi.nlm.nih.gov/pubmed/23750091
http://dx.doi.org/10.6026/97320630009414
_version_ 1782271812202135552
author Carreño-Durán, Luis R
Larios-Serrato, V
Jaimes-Díaz, Hueman
Pérez-Cervantes, Hilda
Zepeda-López, Héctor
Sánchez-Vallejo, Carlos Javier
Olguín-Ruiz, Gabriela Edith
Maldonado-Rodríguez, Rogelio
Méndez-Tenorio, Alfonso
author_facet Carreño-Durán, Luis R
Larios-Serrato, V
Jaimes-Díaz, Hueman
Pérez-Cervantes, Hilda
Zepeda-López, Héctor
Sánchez-Vallejo, Carlos Javier
Olguín-Ruiz, Gabriela Edith
Maldonado-Rodríguez, Rogelio
Méndez-Tenorio, Alfonso
author_sort Carreño-Durán, Luis R
collection PubMed
description 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.
format Online
Article
Text
id pubmed-3670124
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Biomedical Informatics
record_format MEDLINE/PubMed
spelling pubmed-36701242013-06-07 Design of a set of probes with high potential for influenza virus epidemiological surveillance Carreño-Durán, Luis R Larios-Serrato, V Jaimes-Díaz, Hueman Pérez-Cervantes, Hilda Zepeda-López, Héctor Sánchez-Vallejo, Carlos Javier Olguín-Ruiz, Gabriela Edith Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso Bioinformation Hypothesis 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. Biomedical Informatics 2013-04-30 /pmc/articles/PMC3670124/ /pubmed/23750091 http://dx.doi.org/10.6026/97320630009414 Text en © 2013 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Hypothesis
Carreño-Durán, Luis R
Larios-Serrato, V
Jaimes-Díaz, Hueman
Pérez-Cervantes, Hilda
Zepeda-López, Héctor
Sánchez-Vallejo, Carlos Javier
Olguín-Ruiz, Gabriela Edith
Maldonado-Rodríguez, Rogelio
Méndez-Tenorio, Alfonso
Design of a set of probes with high potential for influenza virus epidemiological surveillance
title Design of a set of probes with high potential for influenza virus epidemiological surveillance
title_full Design of a set of probes with high potential for influenza virus epidemiological surveillance
title_fullStr Design of a set of probes with high potential for influenza virus epidemiological surveillance
title_full_unstemmed Design of a set of probes with high potential for influenza virus epidemiological surveillance
title_short Design of a set of probes with high potential for influenza virus epidemiological surveillance
title_sort design of a set of probes with high potential for influenza virus epidemiological surveillance
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670124/
https://www.ncbi.nlm.nih.gov/pubmed/23750091
http://dx.doi.org/10.6026/97320630009414
work_keys_str_mv AT carrenoduranluisr designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT lariosserratov designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT jaimesdiazhueman designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT perezcervanteshilda designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT zepedalopezhector designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT sanchezvallejocarlosjavier designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT olguinruizgabrielaedith designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT maldonadorodriguezrogelio designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance
AT mendeztenorioalfonso designofasetofprobeswithhighpotentialforinfluenzavirusepidemiologicalsurveillance