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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: 0.9.4 (April 2023)

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

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, bioRxiv 2022.10.27.514069; doi: 10.1101/2022.10.27.514069

Conservation analysis algorithm

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 πŸ‡ΈπŸ‡ͺ.
We are open for suggestions to extend and improve uorf4u functionality. Please don't hesitate to share your ideas or feature requests.