PhylArray : Phylogenetic Probe Design Algorithm For MicroArray

摘要: Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access this microbial ‘black-box’, the development of powerful tools microarrays are necessary. However, reliability approach relies on probe efficiency, particular sensitivity, specificity and explorative power, obtain an image communities that close reality. Results: We propose a new design algorithm able select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented program called ‘PhylArray’, designs combination degenerate nondegenerate for each target taxon. Comparative experimental evaluations indicate designed with PhylArray yield higher sensitivity than those by conventional approaches. Applying combined PhyArray/GoArrays strategy helps optimize hybridization performance short probes. Finally, hybridizations environmental targets have shown use can draw attention even previously bacteria. Availability: http://fc.isima.fr/� rimour/phylarray/ Contact: pierre.peyret@univ-bpclermont.fr Supplementary information: data available Bioinformatics online.