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Related Concept Videos

Ribosome Profiling02:24

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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.
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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Riboswitches01:56

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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Updated: Feb 17, 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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InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data.

Eilidh L Ward1,2, Isabel Birds1,2, Mary J O'Connell3,4

  • 1School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.

Bioinformatics Advances
|February 16, 2026
PubMed
Summary
This summary is machine-generated.

InspectorORF is a new R package that visualizes ribosome profiling and RNA sequencing data. This tool aids in validating novel open reading frames (ORFs) and understanding translation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Ribosome profiling has advanced understanding of the translatome, revealing numerous alternative open reading frames (ORFs).
  • Current ORF detection tools lack visual inspection capabilities crucial for validation and prediction of translation.
  • Novel ORFs include out-of-frame, overlapping, upstream, downstream, and non-canonical start codon variants.

Purpose of the Study:

  • To present InspectorORF, an R package for visualizing ribosome profiling and RNA sequencing reads.
  • To facilitate the validation and prediction of novel ORFs by enabling visual inspection of translation data.
  • To integrate diverse evidence, including proteomics and long-read sequencing, for robust ORF validation.

Main Methods:

  • Development of InspectorORF, an R package for data visualization.
  • Integration of ribosome profiling and RNA sequencing reads for comparative analysis.
  • Customizable plotting options to include proteomic and long-read sequencing data.

Main Results:

  • InspectorORF enables the discrimination between transcriptional and translational signals.
  • The package facilitates the validation of predicted novel ORFs through integrated data visualization.
  • Complementary evidence from proteomics and long-read sequencing can be incorporated for enhanced validation.

Conclusions:

  • InspectorORF provides a valuable tool for researchers studying translation and novel ORF discovery.
  • Visual inspection of ribosome profiling data is essential for accurate ORF validation.
  • Integrated analysis of multi-omics data improves the reliability of novel ORF identification.