title: Probe Design Strategies for Oligonucleotide Microarrays.
abstract: Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.
authors.affiliation: Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.affiliation: Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, INRA, AgroParisTech, UMR 782, Thiverval-Grignon, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Dugat-Bony
authors.affiliation: Genomic Platform and R&D, Genoscreen, Campus de l'Institut Pasteur, Lille, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Denonfoux
authors.affiliation: CRRI, Clermont Université, F-63177, Aubière, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Mahul
authors.affiliation: Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France. pierre.peyret@udamail.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D000465:Algorithms; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D011506:Proteins / Q000235:genetics
chemical_list: D015345:Oligonucleotide Probes; D011506:Proteins
keywords: DNA microarrays; Explorative probe; HiSpOD; KASpOD; Probe design