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.
|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 https://quay.io/repository/biocontainers/paralyzer.