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Bioinformatics Advance Access published online on November 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti112
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 15, 2004
Revised October 22, 2004
Accepted October 28, 2004

Article

GoArrays: highly dynamic and efficient microarray probe design

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

1 LIMOS UMR CNRS 6158 - Blaise Pascal University - Clermont-Ferrand II, BP 10125, 63177 Aubiere Cedex, France
2 LBP 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.
Sébastien Rimour, E-mail: rimour{at}isima.fr


  Abstract

Motivation: The use of oligonucleotide microarray technology requires a very detailed attention for 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 condition, especially when dealing with complex target mixture. Indeed, our biological model is a human obligate parasite, the microsporidia Encephalitozoon cuniculi. Targets that are extracted from biological sample 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 far as in the algorithmic point of view. We also present experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos. A specific E. cuniculi microarray will overtake 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/.


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