GoArrays: highly dynamic and efficient microarray probe design

• Published in: Bioinformatics 2005-04, Vol.21 (7), p.1094-1103
• Main Authors: Rimour, Sébastien, Hill, David, Militon, Cécile, Peyret, Pierre
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Biodiversity and Ecology; Bioinformatics; Biological and medical sciences; Computer Science; Computer-Aided Design; Encephalitozoon cuniculi; Encephalitozoon cuniculi - genetics; Encephalitozoon cuniculi - metabolism; Environmental Sciences; Equipment Design; Equipment Design - methods; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; General aspects; Life Sciences; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Microsporidia; Oligonucleotide Array Sequence Analysis; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Probes; Oligonucleotide Probes - genetics; Quantitative Methods; Software; Transcription Factors; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti112

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: [e-mail] for computing part, and [e-mail] for collaborative projects.