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Bioinformatics Advance Access originally published online on November 5, 2004
Bioinformatics 2005 21(7):1094-1103; doi:10.1093/bioinformatics/bti112
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

GoArrays: highly dynamic and efficient microarray probe design

Sébastien Rimour 1,*, David Hill 1, Cécile Militon 2 and Pierre Peyret 2

1LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II BP 10125, 63177 Aubiere Cedex, France
2LBP UMR CNRS 6023, Blaise Pascal University, Institut Universitaire de Technologie, Clermont-Ferrand I University BP 86 63177 Aubiere Cedex, France

*To whom correspondence should be addressed.

Motivation: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex physicochemical constraints. Whereas there are more and more publicly available programs for microarray oligonucleotide design, most of them use the same algorithm or criteria to design oligos, with only little variation.

Results: We show that classical approaches used in oligo design software may be inefficient under certain experimental conditions, especially when dealing with complex target mixtures. Indeed, our biological model is a human obligate parasite, the microsporidia Encephalitozoon cuniculi. Targets that are extracted from biological samples are composed of a mixture of pathogen transcripts and host cell transcripts. We propose a new approach to design oligonucleotides which combines good specificity with a potentially high sensitivity. This approach is original in the biological point of view as well as in the algorithmic point of view. We also present an experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos. A specific E.cuniculi microarray will overcome the difficulty to discriminate the parasite mRNAs from the host cell mRNAs demonstrating the power of the microarray approach to elucidate the lifestyle of an intracellular pathogen using mix mRNAs.

Availability: Our method is implemented in the GoArrays software, available at http://www.isima.fr/bioinfo/goarrays/

Contact: rimour{at}isima.fr for computing part, and pierre.peyret{at}univ-bpclermont.fr for collaborative projects.


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