GoArray: Highly Dynamic and Efficient Microarray Probe Design

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. Despite the widespread use of this technology, there are very few publicly available programs for microarray oligonucleotide design. In this paper, we show that classical approaches used in these programs 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 Encephalitozoon cuniculi transcripts and host cell transcripts. 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 mRNA. 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 implemented it in a program: GoArray that enables the design of specific probes for each gene in an entire genome. We also present experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos.