Splice site identification by idlBNs

Motivation: Computational identification of functional sites in nucleotide sequences is at the core of many algorithms for the analysis of genomic data. This identification is based on the statistical parameters estimated from a training set. Often, because of the huge number of parameters, it is difficult to obtain consistent estimators. To simplify the estimation problem, one imposes independent assumptions between the nucleotides along the site. However, this can potentially limit the minimum value of the estimation error. Results: In this paper, we introduce a novel method in the context of identifying functional sites, that finds a reasonable set of independence assumptions supported by the data, among the nucleotides, and uses it to perform the identification of the sites by their likelihood ratio. More importantly, in many practical situations it is capable of improving its performance as the training sample size increases. We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction.