EvoClustRNA

A clustering routines of evolutionary conserved regions (helical regions) for RNA fold prediction.

At the moment we are testing the approach using models from Rosetta Farna (https://www.rosettacommons.org/) and SimRNAweb (http://genesilico.pl/SimRNAweb/).

THE PAPER IS OUT

Magnus M, Kappel K, Das R, Bujnicki JM. RNA 3D structure prediction guided by independent folding of homologous sequences. BMC Bioinformatics; 2019;:1–15. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3120-y

To install the package, type:

git clone https://github.com/mmagnus/EvoClustRNA.git

To install, type:

pip install --user -r docs/requirements.txt

Name		Name	Last commit message	Last commit date
Latest commit History 165 Commits
benchmark		benchmark
docs		docs
test_data		test_data
test_out/rp14		test_out/rp14
.gitignore		.gitignore
LICENSE.md		LICENSE.md
README.md		README.md
RNAalignment.py		RNAalignment.py
RNAmodel.py		RNAmodel.py
changelog.md		changelog.md
evoClustRNA-demo.ipynb		evoClustRNA-demo.ipynb
evoClustRNA.py		evoClustRNA.py
evoClust_autoclustix.py		evoClust_autoclustix.py
evoClust_calc_rmsd.py		evoClust_calc_rmsd.py
evoClust_clustix.py		evoClust_clustix.py
evoClust_get_models.py		evoClust_get_models.py
install.sh		install.sh
rna_evo_rosetta_run.py		rna_evo_rosetta_run.py
test.sh		test.sh
test_rmsd.sh		test_rmsd.sh