TY - JOUR
T1 - In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification
AU - Méndez-Tenorio, Alfonso
AU - Flores-Cortés, Perla
AU - Guerra-Trejo, Armando
AU - Jaimes-Díaz, Hueman
AU - Reyes-Rosales, Emma
AU - Maldonado-Rodríguez, Arcadio
AU - Espinosa-Lara, Mercedes
AU - Maldonado-Rodríguez, Rogelio
AU - Kenneth, Loren Beattie
PY - 2006/4
Y1 - 2006/4
N2 - 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 pair-wise 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 subtypes.
AB - 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 pair-wise 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 subtypes.
KW - Evaluation
KW - HPV
KW - In silico
KW - UFC
KW - Virtual hybridization
UR - http://www.scopus.com/inward/record.url?scp=34548029765&partnerID=8YFLogxK
M3 - Artículo
C2 - 17578073
AN - SCOPUS:34548029765
SN - 0187-4640
VL - 48
SP - 56
EP - 65
JO - Revista latinoamericana de microbiologia
JF - Revista latinoamericana de microbiologia
IS - 2
ER -