title: In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification.
abstract: The identification of microorganisms by whole genome DNA fingerprinting was tested "in silico". 94 HPV genome sequences were submitted to virtual hybridization analysis on a DNA chip with 342 probes. This Universal Fingerprinting Chip (UFC) constitutes a representative set of probes of all the possible 8-mer sequences having at least two internal and non contiguous sequence differences between all them. A virtual hybridization analysis was performed in order to find the fingerprinting pattern that represents the signals produced for the hybridization of the probes allowing at most a single mismatch. All the fingerprints for each virus were compared against each other in order to obtain all the pairwise distances measures. A match-extension strategy was applied to identify only the shared signals corresponding to the hybridization of the probes with homologous sequences between two HPV genomes. A phylogenetic tree was constructed from the fingerprint distances using the Neighbor-Joining algorithm implemented in the program Phylip 3.61. This tree was compared with that produced from the alignment of whole genome HPV sequences calculated with the program Clustal_X 1.83. The similarities between both trees are suggesting that the UFC-8 is able to discriminate accurately between viral genomes. A fingerprint comparative analysis suggests that the UFC-8 can differentiate between HPV types and sub-types.
authors.affiliation: Laboratorio de Tecnología del DNA, Escuela Nacional de Ciencias Biológicas. IPN. Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, 11340, Mexico DF.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Méndez-Tenorio
authors.forename: Perla
authors.initials: P
authors.lastname: Flores-Cortés
authors.forename: Armando
authors.initials: A
authors.lastname: Guerra-Trejo
authors.forename: Hueman
authors.initials: H
authors.lastname: Jaimes-Díaz
authors.forename: Emma
authors.initials: E
authors.lastname: Reyes-Rosales
authors.forename: Arcadio
authors.initials: A
authors.lastname: Maldonado-Rodríguez
authors.forename: Mercedes
authors.initials: M
authors.lastname: Espinosa-Lara
authors.forename: Rogelio
authors.initials: R
authors.lastname: Maldonado-Rodríguez
authors.forename: Loren Beattie
authors.initials: LB
authors.lastname: Kenneth
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods*; D015344:DNA Probes, HPV; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D015344:DNA Probes, HPV