Bioinformatic Analysis of Splicing Events

The sequencing of large amounts of human genomic and cDNA samples has resulted in the identification of an increasing number of sequence variations. Especially when the samples are related to a certain phenotype or a pathological state, the question arises whether these sequence variants have a functional significance. Splicing regulatory sequences have been identified by various experimental and bioinformatic approaches, and these data have been incorporated into several web-based programs. In this chapter, the first step of the analysis of a mutation in the pre-mRNA is described, whereby several available computer programs are used to generate a hypothesis regarding the pre-mRNA's possible functional role. The programs are quite accurate when predicting the effect of a mutation in a splice site, but the predictions of other splicing regulatory sequences are less accurate. However, a bioinformatic analysis results in hypotheses that can be tested experimentally. It should be pointed out that all bioinformatic predictions require experimental validation.