Analysis of degradome (AKA Parallel Analysis of RNA Ends [PARE]) data to find sliced miRNA and siRNA targets

Download latest version from github at

  • System requirements: a BASH-like command line
  • Dependencies: Perl, R, the Math::CDF perl module, samtools, bowtie, bowtie-build, RNAplex, and (included with CleaveLand4).
  • Current Version: 4.3 (Nov. 7, 2013)
  • Major changes:  Single command analysis, including read alignment and putative target site identification. Putative target sites now more sensitive and based on RNA-RNA thermodyamics (via RNAplex) instead of sequence aligners.
  • Tutorial with sample data available.


  • The original CleaveLand paper was Addo-Quaye, C., Miller, W., and Axtell, M.J.  (2009).  CleaveLand:  A pipeline for using degradome data to find cleaved small RNA targets.  Bioinformaticsdoi: 10.1093/bioinformatics/btn604
  • CleaveLand4 (which works quite differently than the original from the 2009 paper) was first cited in: A non-canonical plant microRNA target site Brousse C, Liu Q, Beuclair L, Deremetz A, Axtell MJ, Bouché N.  (2014). Nucleic Acids Research doi:10.1093/nar/gku157