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 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.
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. hjaimesd@ipn.mx.
Hueman
H
Jaimes-Díaz
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. siedracko@hotmail.com.
Violeta
V
Larios-Serrato
Institute of Epidemiological Diagnosis & Reference, Mexico City 01480, Mexico. lloretys@gmail.com.
Teresa
T
Lloret-Sánchez
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. golguinr@ipn.mx.
Gabriela
G
Olguín-Ruiz
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. cjsanchezv@ipn.mx.
Carlos
C
Sánchez-Vallejo
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. lcarreno@ipn.mx.
Luis
L
Carreño-Durán
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. romaldo_dr@hotmail.com.
Rogelio
R
Maldonado-Rodríguez
Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, National Polytechnic Institute, Mexico City 11340, Mexico. amendezt@ipn.mx.
Alfonso
A
Méndez-Tenorio
Bacillus anthracis genomic fingerprints; DNA microarrays; virtual hybridization