In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification
Méndez-Tenorio, A.; Flores-Cortés, P.; Guerra-Trejo, A.; Jaimes-Díaz, H.; Reyes-Rosales, E.; Maldonado-Rodríguez, A.; Espinosa-Lara, M.; Maldonado-Rodríguez, R.; Kenneth, L.B.
Revista Latinoamericana de Microbiologia 48(2): 56-65
2006
ISSN/ISBN: 0187-4640 PMID: 17578073 Document Number: 599905
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.