uORF4u is a bioinformatics tool for conserved upstream ORF annotation.
Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, configs, argparse, pandas, statistics, logomaker, matplotlib, reportlab.
Python version: >= 3.7
OS-level dependencies: mafft (v7.490 is included in the package)
Version: 0.9.5 (May 2023)
Web version is available at the Atkinson Lab Server Portal: server.atkinson-lab.com/uorf4u
Data analysis pipeline
- The most stable release of uorf4u can be installed directly from pypi:
python3 -m pip install uorf4u
- The development version is available at github :
git clone https://github.com/GCA-VH-lab/uorf4u.git cd uorf4u python3 -m pip install --upgrade pip python3 -m pip install wheel python3 setup.py sdist bdist_wheel python3 -m pip install -e .
! If you're a linux user, run
uorf4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.
If you find uorf4u useful, please cite:
Artyom. A. Egorov, Gemma C. Atkinson, uORF4u: a tool for annotation of conserved upstream open reading frames, Bioinformatics, Volume 39, Issue 5, May 2023, btad323; doi: 10.1093/bioinformatics/btad323
Conservation analysis algorithm
uORF4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden 🇸🇪.
We are open for suggestions to extend and improve uorf4u functionality. Please don't hesitate to share your ideas or feature requests.