AgeWa: An integrated approach for antisense experiment design

The new experimental methods for gene expression analysis, such as those based on the microarray technology, require a subsequent validation of the gene function, that can be carried out by means of either in vitro or in vivo models. One of the most promising methodologies that have been proposed in the last decade for the investigation of gene function is based on antisense oligonucleotides [ASO]. In antisense experiment design, the crucial step is the characterization of nucleotide domains that can efficiently be targeted by this synthetic molecule. At present, no standard procedures are available for target selection. In this paper, we propose an integrative approach for ASO target selection. The proposed tool, AgeWa (Automatic Gene Walk), combines a neural filter with database mining in order to predict the optimal target for antisense action.