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.

PARalyzer executables can be dowloaded here:
PARalyzer v1.5, README, Version 1.5 is also able to parse SAM/BAM files.
PARalyzer v1.1, README

PARalyzer source code can can be downloaded here:
PARalyzer v1.5
PARalyzer v1.1
Note: PARalyzer is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.

We also provide the filter files for human assembly hg19 here and mouse assembly mm9 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).