Description

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)
License: CC0
Version: 0.9.5 (May 2023)

Web version is available at the Atkinson Lab Server Portal: server.atkinson-lab.com/uorf4u

Detailed documentation

Data analysis pipeline:

Installation 🛠️

• 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.

Reference 📃

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

Contact 📇

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!

Authors 👨🏻‍💻

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 svist4get functionality. Please don't hesitate to share your ideas or feature requests.