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

ABSTRACT:

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. We cross-validate PEKA with mCross and show that the use of input control for background correction is not required to yield high specificity of enriched motifs. We identify motif cla

SUBMITTER: Kuret K 

PROVIDER: S-EPMC9461102 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature