PhylArray: phylogenetic probe design algorithm for microarray

• Published in: Bioinformatics Vol. 23; no. 19; pp. 2550 - 2557
• Main Authors: Militon, Cécile, Rimour, Sébastien, Missaoui, Mohieddine, Biderre, Corinne, Barra, Vincent, Hill, David, Moné, Anne, Gagne, Geneviève, Meier, Harald, Peyretaillade, Eric, Peyret, Pierre
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.10.2007; Oxford Publishing Limited (England); Oxford University Press (OUP)
• Subjects: Algorithms; Base Sequence; Biodiversity and Ecology; Bioinformatics; Biological and medical sciences; DNA Probes - genetics; Environmental Sciences; Fundamental and applied biological sciences. Psychology; Gene Targeting - methods; General aspects; In Situ Hybridization - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Microbial activity; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis - methods; Probes; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software; Design; Phylogeny; Microarray; Algorithm; Bioinformatics; bioinformatique; DNA microarrays; biodiversity; microorganisms; bioinformatics; phylogeny; microorganismes; phylogénie; Biopuces ADN; biodiversite
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btm392

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. Availability: http://fc.isima.fr/~rimour/phylarray/ Contact: pierre.peyret@univ-bpclermont.fr Supplementary information: Supplementary data are available at Bioinformatics online.