We developed the PARalyzer algorithm to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol.The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites. Analysis of previously published data sets shows that we delineate sites at high resolution and signal-to-noise ratio across different RNA binding proteins.
The source for PARalyzer v1.0 can be downloaded here.
Evidence ranked motif analysis of the PARalyzer generated interaction sites can be performed using cERMITv1.1 (sequence-specific RBPs) or mEATv1.0 (Argonaute PAR-CLIP).