Comparing translation of open reading frames within individual transcripts

RIBOSS consists of Python modules for analysis of ribosome profiling data for prokaryotes and eukaryotes. See the use cases and benchmarking results here.

User guide

Install Miniforge3 and create a conda environment

wget https://github.com/conda-forge/miniforge/releases/download/24.7.1-2/Miniforge3-24.7.1-2-Linux-x86_64.sh
bash Miniforge3-24.7.1-2-Linux-x86_64.sh -b -p $HOME/miniforge3
eval "$(/$HOME/miniforge3/bin/conda shell.bash hook)" # your terminal prompt will show (base) bash-5.1$

Install RIBOSS

git clone https://github.com/lcscs12345/riboss.git
cd riboss
conda env create -f environment.yml
conda activate riboss # your terminal prompt will show (riboss) bash-5.1$
DIRNAME=`which python | xargs dirname`
cp bin/riboprof $DIRNAME
chmod +x $DIRNAME/riboprof
which python | awk 'sub(/python/,"pip3") {print $1, "install -e ."}' | sh # editable mode

Activate the conda environment for next time

eval "$(/$HOME/miniforge3/bin/conda shell.bash hook)"
conda activate riboss

Basic usage

from riboss.orfs import translate
na='ATGGTCTGA'
translate(na)

You should see 'MV'.

References:

• Lim, C. S., & Brown, C. M. (2024). RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling. BioRxiv, DOI: 10.1101/2024.11.07.622529
• Lim, C.S., Wardell, S.J.T., Kleffmann, T. & Brown, C.M. (2018) The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res, 46:4575-4591. DOI: 10.1093/nar/gky282