In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification.
Rev Latinoam Microbiol
; 48(2): 56-65, 2006.
Article
em En
| MEDLINE
| ID: mdl-17578073
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Sondas de DNA de HPV
/
Impressões Digitais de DNA
/
Análise de Sequência com Séries de Oligonucleotídeos
Tipo de estudo:
Diagnostic_studies
/
Evaluation_studies
Idioma:
En
Revista:
Rev Latinoam Microbiol
Ano de publicação:
2006
Tipo de documento:
Article
País de publicação:
México