PARalyzer (PAR-CLIP data analyzer)
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 PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol.The use of photoactivatable nucleotides in the PAR-CLIP protocol results in 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, providing for single-nucleotide resolution binding information. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.
See the PARalyzer publication for more information.
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).