Difference between revisions of "Paralyzer"

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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|paralyzer}} |{{#vardefine:url|https://ohlerlab.mdc-berlin.de/software/PARaly...")
 
m (Israel.herrera moved page PARalyzer to Paralyzer)
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
+
* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_CONF - parameters directory
+
* HPC_{{uc:{{#var:app}}}}_CONF - parameters directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 18:19, 27 May 2022

Description

paralyzer website  

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.

Environment Modules

Run module spider paralyzer to find out what environment modules are available for this application.

System Variables

  • HPC_PARALYZER_DIR - installation directory
  • HPC_PARALYZER_BIN - executable directory
  • HPC_PARALYZER_DOC - documentation directory
  • HPC_PARALYZER_CONF - parameters directory