RT Journal Article SR Electronic T1 uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames JF bioRxiv FD Cold Spring Harbor Laboratory SP 415018 DO 10.1101/415018 A1 Anica Scholz A1 Florian Eggenhofer A1 Rick Gelhausen A1 Björn Grüning A1 Kathi Zarnack A1 Bernhard Brüne A1 Rolf Backofen A1 Tobias Schmid YR 2019 UL http://biorxiv.org/content/early/2019/03/13/415018.abstract AB Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools identifies uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.