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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.
The technique...
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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Leaky Scanning02:28

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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: Aug 5, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.

Ales Varabyou1,2, Beril Erdogdu1,3, Steven L Salzberg1,2,3,4

  • 1Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.

Biorxiv : the Preprint Server for Biology
|March 30, 2023
PubMed
Summary

ORFanage identifies open reading frames (ORFs) in RNA sequencing data, improving gene transcript annotation and discovering novel protein variants. This fast system enhances biological understanding by separating signal from noise in large datasets.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Transcriptome assembly methods often lack robust open reading frame (ORF) identification capabilities.
  • Accurate ORF annotation is crucial for understanding gene function and identifying novel protein variants.

Conclusions:

  • ORFanage is an efficient tool for ORF identification in transcriptome assemblies.
  • It aids in distinguishing transcriptional signal from noise and identifying functional variants.
  • The system advances biological and medical research through improved transcript annotation and variant discovery.