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Revista Latinoamericana de Microbiología

2006, Number 2

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Microbiología 2006; 48 (2)

In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification

Méndez TA, Flores CP, Guerra TA, Jaimes DH, Reyes RE, Maldonado RA, Espinosa LM, Maldonado RR, Beattie KL

Language: English
References: 40
Page: 56-65
PDF size: 182.67 Kb.


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 subtypes.


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