In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fi...

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Main Authors:	Jaimes-Díaz, Hueman, Larios-Serrato, Violeta, Lloret-Sánchez, Teresa, Olguín-Ruiz, Gabriela, Sánchez-Vallejo, Carlos, Carreño-Durán, Luis, Maldonado-Rodríguez, Rogelio, Méndez-Tenorio, Alfonso
Format:	Online
Language:	English
Published:	MDPI 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996382/

id	pubmed-4996382
recordtype	oai_dc
spelling	pubmed-49963822016-09-06 In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization Jaimes-Díaz, Hueman Larios-Serrato, Violeta Lloret-Sánchez, Teresa Olguín-Ruiz, Gabriela Sánchez-Vallejo, Carlos Carreño-Durán, Luis Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso Article In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray. Two virtual hybridization methods were used: the Direct and the Extended method to identify the number of potential hybridization sites and thus determine the minimum sensitivity value to discriminate between genomes with 99.9% similarity. Genomic fingerprints were compared using both methods and phylogenomic trees were constructed to verify that the minimum detection value is 0.000017. Results obtained from the genomic fingerprints suggest that the distribution in the trees is correct, as compared to other taxonomic methods. Specific virtual hybridization sites for each of the genomes studied were also identified. MDPI 2015-02-17 /pmc/articles/PMC4996382/ /pubmed/27600214 http://dx.doi.org/10.3390/microarrays4010084 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Jaimes-Díaz, Hueman Larios-Serrato, Violeta Lloret-Sánchez, Teresa Olguín-Ruiz, Gabriela Sánchez-Vallejo, Carlos Carreño-Durán, Luis Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso
spellingShingle	Jaimes-Díaz, Hueman Larios-Serrato, Violeta Lloret-Sánchez, Teresa Olguín-Ruiz, Gabriela Sánchez-Vallejo, Carlos Carreño-Durán, Luis Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
author_facet	Jaimes-Díaz, Hueman Larios-Serrato, Violeta Lloret-Sánchez, Teresa Olguín-Ruiz, Gabriela Sánchez-Vallejo, Carlos Carreño-Durán, Luis Maldonado-Rodríguez, Rogelio Méndez-Tenorio, Alfonso
author_sort	Jaimes-Díaz, Hueman
title	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
title_short	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
title_full	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
title_fullStr	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
title_full_unstemmed	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
title_sort	in silico genomic fingerprints of the bacillus anthracis group obtained by virtual hybridization
description	In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray. Two virtual hybridization methods were used: the Direct and the Extended method to identify the number of potential hybridization sites and thus determine the minimum sensitivity value to discriminate between genomes with 99.9% similarity. Genomic fingerprints were compared using both methods and phylogenomic trees were constructed to verify that the minimum detection value is 0.000017. Results obtained from the genomic fingerprints suggest that the distribution in the trees is correct, as compared to other taxonomic methods. Specific virtual hybridization sites for each of the genomes studied were also identified.
publisher	MDPI
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996382/
_version_	1613633825112326144

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

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