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RNA-seq03:21

RNA-seq

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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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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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Related Experiment Video

Updated: Feb 28, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

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isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization.

Ko Ikemoto1, Akihiro Fujimoto1

  • 1Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.

Bioinformatics Advances
|February 27, 2026
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Summary

Long-read RNA sequencing reveals complex transcriptomes. The new isoespy pipeline integrates isoform structure, expression, and function, aiding the analysis of hepatocellular carcinoma to understand protein diversity.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Long-read RNA sequencing (RNA-seq) offers deep insights into transcriptome diversity.
  • Understanding the functional roles of individual RNA isoforms remains a challenge.

Purpose of the Study:

  • To introduce isoespy, a novel bioinformatics pipeline.
  • To integrate isoform structure, differential expression, and functional annotations for long-read RNA-seq data.

Main Methods:

  • isoespy integrates open reading frame predictors.
  • It juxtaposes isoform expression levels with gene models.
  • The pipeline visualizes user-provided positional and non-positional features.

Main Results:

  • Application to hepatocellular carcinoma data revealed isoform usage differences.
  • Analysis identified variations in predicted protein function.
  • isoespy facilitates interpretation of transcriptomic complexity.

Conclusions:

  • isoespy provides integrated structural and functional visualization for transcriptomic data.
  • The pipeline aids in understanding isoform-level functional diversity.
  • This tool enhances the analysis of complex transcriptomes from long-read RNA-seq.