Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays.

ABSTRACT:

Background

Alternative splicing of exons in a pre-mRNA transcript is an important mechanism which contributes to protein diversity in human. Arrays for detecting alternative splicing are available using several different probe designs, including those based on exon-junctions. In this work, we introduce a new method for predicting alternatively skipped exons from exon-junction arrays. Predictions based on our method are compared against controls and their sequences are analyzed to identify motifs important for regulating alternative splicing.

Results

Our comparison of several alternative methods shows that an exon-skipping score based on neighboring junctions best discriminates between positive and negative controls. Sequence analysis of our predicted exons confirms the prese

SUBMITTER: Kechris K 

PROVIDER: S-EPMC2631580 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature