Axtell Lab - Software
CleaveLand
CleaveLand is a command-line executed pipeline for finding cleaved small RNA targets using degradome data (also known as PARE [parallel analysis of RNA ends] and GMUCT [genome-wide mapping of uncapped transcripts]). Provided with a set of degradome data, a list of small RNA queries, a reference transcriptome/mRNA set, CleaveLand outputs potentially cleaved small RNA targets along with other supporting information.
System Requirements :: Linux/UNIX OS, at least 2GB RAM
README.txt (8K)
LICENSE.txt (34K; GNU Public License -- free for all)
CleaveLand_1-5.9.tar.gz (68K; Current Version = 1.5.9)
Sample Input Data :: To test an installation and to demonstrate file formatting conventions, we provide the file TestData.tar.gz, which is a short batch of Arabidopsis thaliana degradome data, two miRNA queries, and a set of A. thaliana rRNAs (for filtering purposes). NOTE: A copy of A. thaliana transcripts needs to be also obtained for testing with these sample data! (NOT provided within TestData.tar.gz ! -- see the link below).
TestData.tar.gz (2.0M)
Citation :: If you use CleaveLand in your work, please cite:
Addo-Quaye, C., Miller, W., and Axtell, M.J. (2009). CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25: 130-131. (epub Nov 18 2008)
Disclaimer :: Software is provided in an “as-is” condition. We (MJ Axtell, lab members, Pennsylvania State University) make no guarantees for performance. Download and use of software on this page indicates your agreement that we cannot be held liable for any resulting damages.
Updated: 4 November 2009 MJA