PhylArray: phylogenetic probe design algorithm for microarray

Cécile Militon (1) , Sébastien Rimour (1) , Mohieddine Missaoui (2) , Corinne Biderre (1) , Vincent Barra (2) , David R.C. Hill (2) , Anne Moné (1) , Geneviève Gagne (1) , Harald Meier (3) , Eric Peyretaillade (1) , Pierre Peyret (1)

1 LMGE - Laboratoire Microorganismes : Génome et Environnement
2 LIMOS - Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes
3 Department of Informatics of the Technische Universität München

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.

Mots clés: biodiversite; biodiversity; phylogénie; phylogeny; microorganismes; microorganisms; bioinformatique; bioinformatics; Biopuces ADN; DNA microarrays

Domaines: Biodiversité et Ecologie

Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, et al.. PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics, 2007, 23 (19), pp.2550-7. ⟨10.1093/bioinformatics/btm392⟩. ⟨hal-00461398⟩