A program for folding RNA using constraints from proximity ligation experiments.
RNA proximity ligation methods such as CLASH, HiCLIP, PARIS, SPLASH, and COMRADES generate chimeric reads that represent RNA-RNA interactions.
Comrades inputs a set of mapped chimeric reads (produced by hyb, https://github.com/gkudla/hyb), and outputs a ranked list of predicted basepairs. It then combines these basepairs into short structural elements, ranks the elements by number of supporting chimeric reads, and uses the ranked elements as constraints for RNA folding. The output is an RNA structure or set of structures in UNAFold .ct format or vienna dot-bracket format.
Linux operating system
Perl version 5
UNAFold http://unafold.rna.albany.edu/?q=DINAMelt/software
# download package:
wget https://github.com/gkudla/comrades/archive/master.zip
unzip master.zip
mv comrades-master/ comrades
# or clone using git:
git clone https://github.com/gkudla/comrades.git
Add installation location to your PATH:
export PATH=comrades/bin:$PATH
To test the programs, first copy the example input files from comrades/data into a folder of your choice, then run the commands below. Typical run time on the test data is 1 minute for comradesMakeConstraints, and 7 minutes for comradesFold.
generate folding constraints
comradesMakeConstraints -i testData.hyb -f Zika.fasta -b 3324 -e 4521
fold RNA using constraints
comradesFold -c testData.3324-4521_folding_constraints.txt -i Zika_3324-4521.fasta
fold RNA 1,000 times (requires computer cluster running qsub)
qsub comradesFold -c testData.3324-4521_folding_constraints.txt -i Zika_3324-4521.fasta -s 1
# input folding constraints:
testData.3324-4521_folding_constraints.txt
# a subset of mutually compatible folding constraints used to generate the folded structure:
testData.3324-4521_folding_constraints.txt.accepted
# folded RNA in hybrid-ss-min .ct format:
Zika_3324-4521.fasta.ct
# folded RNA in vienna dot-bracket format:
Zika_3324-4521.fasta.vienna
- Grzegorz Kudla, Marta Gabryelska 2018
This project is licensed under the GNU General Public License v3 - see the LICENSE.md file for details