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Updated: Nov 11, 2025
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
3.9K
Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.
Dermot Harnett1, Eelco Meerdink1, Lorenzo Calviello2
1IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
Methods in Molecular Biology (Clifton, N.J.)
|March 25, 2021
Summary
Ribosome profiling (Ribo-seq) identifies actively translated regions. The ORFquant R package uses ribosome distribution to robustly measure translation and distinguish translated from non-translated transcripts.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Ribosome profiling (Ribo-seq) offers precise mapping of actively translating ribosomes.
- Identifying translated open reading frames (ORFs) is crucial for understanding gene expression.
- Existing methods may struggle with complex genomic regions and distinguishing translated from non-translated transcripts.
Purpose of the Study:
- To introduce the ORFquant R package for robustly measuring translation using Ribo-seq data.
- To leverage the periodic distribution of ribosomes for sensitive translation detection.
- To develop a method that handles complex loci and differentiates translated transcripts.
Main Methods:
- Utilized the RiboTaper pipeline and the ORFquant R package.
- Leveraged the periodic distribution of ribosomes along open reading frames (ORFs).
- Applied statistical methods robust to aperiodic noise for translation measurement.
Main Results:
- ORFquant provides a statistically robust measure of translation.
- The method is insensitive to aperiodic noise.
- Successfully distinguished actively translated transcripts from non-translated ones within gene loci.
- Accounted for complex loci with overlapping ORFs.
Conclusions:
- ORFquant offers a powerful and statistically robust tool for analyzing Ribo-seq data.
- The package enhances the ability to identify and quantify translated ORFs.
- This method improves the understanding of translational regulation and gene expression complexity.
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