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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Ribosomal RNA Synthesis02:53

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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Related Experiment Video

Updated: Jan 6, 2026

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

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Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo.

Hsin-Yen Larry Wu1, Isaiah D Kaufman1, Polly Yingshan Hsu2

  • 1Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 16, 2025
PubMed
Summary

We developed a bioinformatics pipeline to find and visualize novel translated small open reading frames (sORFs) using Ribo-seq data. This tool helps uncover hidden sORFs and their functions in gene regulation.

Keywords:
Ribo-seqRiboTaperRibosome profilingSmall ORFsTranscriptome assemblyggRibo

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Small open reading frames (sORFs) are crucial for cellular regulation but are often missed in genome annotations.
  • Translational activity of sORFs is implicated in noncoding RNA biogenesis and signaling pathways.
  • Accurate identification of translated sORFs is challenging due to their small size and lack of canonical features.

Purpose of the Study:

  • To present a novel bioinformatics pipeline for identifying and visualizing translated sORFs from Ribo-seq data.
  • To enable the discovery of previously unannotated sORFs in Arabidopsis.
  • To provide a framework for functional characterization of novel sORFs.

Main Methods:

  • Integration of Ribo-seq/RNA-seq preprocessing and mapping.
  • Optional transcriptome assembly for detecting unannotated transcripts.
  • ORF discovery using RiboTaper and visualization with the ggRibo gene viewer.

Main Results:

  • A comprehensive pipeline for Ribo-seq data analysis was established.
  • The pipeline facilitates the discovery and high-resolution visualization of translated sORFs.
  • Demonstrated utility in Arabidopsis for uncovering hidden sORFs.

Conclusions:

  • The developed pipeline offers a powerful approach for systematic sORF identification and visualization.
  • This method aids in the discovery and future functional studies of novel sORFs.
  • The pipeline is adaptable for sORF discovery across various organisms.