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Article

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

1
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico
2
Institute of Epidemiological Diagnosis & Reference, Mexico City 01480, Mexico
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Heather J. Ruskin
Microarrays 2015, 4(1), 84-97; https://doi.org/10.3390/microarrays4010084
Received: 21 October 2014 / Revised: 12 February 2015 / Accepted: 13 February 2015 / Published: 17 February 2015
(This article belongs to the Special Issue Computational Modeling and Analysis of Microarray Data: New Horizons)
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. View Full-Text
Keywords: Bacillus anthracis genomic fingerprints; virtual hybridization; DNA microarrays Bacillus anthracis genomic fingerprints; virtual hybridization; DNA microarrays
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MDPI and ACS Style

Jaimes-Díaz, H.; Larios-Serrato, V.; Lloret-Sánchez, T.; Olguín-Ruiz, G.; Sánchez-Vallejo, C.; Carreño-Durán, L.; Maldonado-Rodríguez, R.; Méndez-Tenorio, A. In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization. Microarrays 2015, 4, 84-97. https://doi.org/10.3390/microarrays4010084

AMA Style

Jaimes-Díaz H, Larios-Serrato V, Lloret-Sánchez T, Olguín-Ruiz G, Sánchez-Vallejo C, Carreño-Durán L, Maldonado-Rodríguez R, Méndez-Tenorio A. In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization. Microarrays. 2015; 4(1):84-97. https://doi.org/10.3390/microarrays4010084

Chicago/Turabian Style

Jaimes-Díaz, Hueman, Violeta Larios-Serrato, Teresa Lloret-Sánchez, Gabriela Olguín-Ruiz, Carlos Sánchez-Vallejo, Luis Carreño-Durán, Rogelio Maldonado-Rodríguez, and Alfonso Méndez-Tenorio. 2015. "In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization" Microarrays 4, no. 1: 84-97. https://doi.org/10.3390/microarrays4010084

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