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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.
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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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RNA-seq03:21

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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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Types of RNA01:20

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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

Updated: Apr 15, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Identification of protein coding regions in RNA transcripts.

Shiyuyun Tang1, Alexandre Lomsadze2, Mark Borodovsky3

  • 1School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

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|April 15, 2015
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GeneMarkS-T is a new tool for identifying protein-coding regions in RNA transcripts using next-generation sequencing data. It accurately predicts gene structures, even with assembly errors, outperforming existing methods.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Massive parallel sequencing, or RNA-Seq, generates crucial data for eukaryotic gene discovery.
  • Gene identification from RNA transcripts can be achieved through alignment-free or alignment-based methodologies.

Purpose of the Study:

  • To introduce GeneMarkS-T, a novel tool for ab initio identification of protein-coding regions within RNA transcripts.
  • To evaluate the robustness and accuracy of GeneMarkS-T, particularly in predicting translation initiation sites.

Main Methods:

  • GeneMarkS-T employs an algorithm with parameters estimated via unsupervised training, eliminating the need for manually curated training sets.
  • The tool was tested on both modelled and assembled transcripts to assess its performance.

Main Results:

  • Unsupervised training in GeneMarkS-T demonstrates robustness against transcript assembly errors.
  • GeneMarkS-T exhibits superior accuracy in identifying protein-coding regions and predicting translation initiation sites compared to existing methods.

Conclusions:

  • GeneMarkS-T offers a reliable and accurate solution for gene finding in RNA transcripts.
  • The tool's ability to handle assembly errors and its high prediction accuracy make it valuable for eukaryotic gene discovery.