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Related Experiment Video

Updated: Aug 15, 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

Accurate isoform discovery with IsoQuant using long reads.

Andrey D Prjibelski^1,2, Alla Mikheenko³, Anoushka Joglekar^4,5,6

¹Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia. andrewprzh@gmail.com.

Nature Biotechnology

|January 2, 2023

Summary

IsoQuant is a new computational tool that accurately reconstructs gene transcripts from long-read RNA data. It significantly reduces errors in novel transcript discovery for genome annotation.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate genome annotation and transcript isoform determination from long-read RNA sequencing are critical for understanding gene expression.
Existing computational tools face challenges in precisely identifying novel transcripts and alternative splicing events.

Purpose of the Study:

To introduce IsoQuant, a novel computational tool designed for accurate transcript reconstruction from long-read RNA sequencing data.
To evaluate IsoQuant's performance in both reference-based and reference-free genome annotation modes.

Main Methods:

Development of IsoQuant, a tool utilizing intron graphs for transcript reconstruction.
Application of IsoQuant to analyze Oxford Nanopore and Pacific Biosciences long-read RNA data.

Main Results:

IsoQuant accurately reconstructs transcripts, with or without reference genome annotation.
For novel transcript discovery, IsoQuant achieved a fivefold reduction in false positives for Oxford Nanopore reference-based analysis.
IsoQuant demonstrated a 2.5-fold false-positive rate reduction in Oxford Nanopore reference-free mode and improved Pacific Biosciences data analysis.

Conclusions:

IsoQuant offers a robust solution for accurate transcript reconstruction and novel transcript discovery.
The tool enhances the reliability of genome annotation using long-read RNA sequencing data.