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Updated: Dec 10, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

CONCUR: quick and robust calculation of codon usage from ribosome profiling data.

Michaela Frye¹, Susanne Bornelöv²

¹Cell Biology and Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Bioinformatics (Oxford, England)

|September 1, 2020

Summary

This summary is machine-generated.

CONCUR is a new tool for analyzing codon usage in ribosome profiling data. It estimates codon counts at key ribosome positions using aligned sequencing reads.

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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

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Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Ribosome profiling is a key technique for studying gene expression at the translational level.
Understanding codon usage bias is crucial for deciphering translational regulation and efficiency.
Existing tools may not fully capture codon-level dynamics within the ribosome.

Purpose of the Study:

To introduce CONCUR, a novel standalone tool for detailed codon usage analysis.
To enable precise estimation of codon counts at specific ribosome-protected fragment (RPF) sites.
To facilitate the analysis of ribosome dynamics during translation.

Main Methods:

CONCUR processes aligned sequencing reads in Binary Alignment Map (BAM) format.
The tool quantifies codon counts at the E-, P-, and A-sites of the ribosome.
It also analyzes codon counts at positions flanking the A-site.

Main Results:

CONCUR provides site-specific codon count estimations from ribosome profiling data.
The tool allows for in-depth analysis of codon usage patterns within the translating ribosome.
Enables a more granular understanding of translational efficiency and regulation.

Conclusions:

CONCUR offers a valuable addition to the bioinformatics toolkit for ribosome profiling analysis.
The tool facilitates the investigation of codon-level translational control mechanisms.
CONCUR supports research into the intricacies of gene expression and protein synthesis.