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Bioinformatics Advance Access originally published online on August 12, 2007
Bioinformatics 2007 23(19):2550-2557; doi:10.1093/bioinformatics/btm392
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PhylArray: phylogenetic probe design algorithm for microarray

Cécile Militon 1,{dagger}, Sébastien Rimour 1,2,{dagger}, Mohieddine Missaoui 1,2, Corinne Biderre 1, Vincent Barra 2, David Hill 2, Anne Moné 1, Geneviève Gagne 1, Harald Meier 3, Eric Peyretaillade 1 and Pierre Peyret 1,*

1Génomique Intégrée des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des Cézeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubière Cedex, France and 3Lehrstuhl für Rechnertechnik und Rechnerorganisation, Institut für Informatik, Technische Universität München, Germany

*To whom correspondence should be addressed.


  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.

Availability: http://fc.isima.fr/~rimour/phylarray/

Contact: pierre.peyret{at}univ-bpclermont.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Thomas Lengauer

Received on April 3, 2007; revised on July 18, 2007; accepted on July 27, 2007

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