PhylArray: phylogenetic probe design algorithm for microarray.
Bioinformatics
; 23(19): 2550-7, 2007 Oct 01.
Article
em En
| MEDLINE
| ID: mdl-17698494
ABSTRACT
MOTIVATION Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. RESULTS:
We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Software
/
Sondas de DNA
/
Análise de Sequência de DNA
/
Hibridização In Situ
/
Marcação de Genes
/
Análise de Sequência com Séries de Oligonucleotídeos
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2007
Tipo de documento:
Article