Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.

Background: Crosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA-protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins (RBPs), it is important to understand to what degree the enriched motifs specify the RNA-binding profiles of RBPs in cells.

Results: We develop positionally enriched k-mer analysis (PEKA), a computational tool for efficient analysis of enriched motifs from individual CLIP datasets, which minimizes the impact of technical and regional genomic biases by internal data normalization.