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.

Versions 1.5
License PARalyzer is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install paralyzer

and update with:

conda update paralyzer


A Docker container is available at