Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

12.1K
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...
12.1K
Nuclear Fusion02:45

Nuclear Fusion

33.9K
The process of converting very light nuclei into heavier nuclei is also accompanied by the conversion of mass into large amounts of energy, a process called fusion. The principal source of energy in the sun is a net fusion reaction in which four hydrogen nuclei fuse and ultimately produce one helium nucleus and two positrons.
A helium nucleus has a mass that is 0.7% less than that of four hydrogen nuclei; this lost mass is converted into energy during the fusion. This reaction produces about...
33.9K
RNA Interference01:23

RNA Interference

28.2K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
28.2K
RNA Splicing01:32

RNA Splicing

60.7K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
60.7K
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

27.1K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
27.1K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

32.8K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
32.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.

Bioinformatics (Oxford, England)·2026
Same author

Precision-guided therapy in H3K27-altered diffuse midline glioma.

Nature communications·2026
Same author

Long-read sequencing-based atlas of tissue-specific expression of DNM1L transcript variants.

The FEBS journal·2026
Same author

Comprehensive Multiplatform Tyrosine Kinase Profiling Reveals Novel Actionable FGFR Aberrations across Sarcomas Affecting the Young.

Molecular cancer therapeutics·2026
Same author

Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung.

Mucosal immunology·2026
Same author

Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across sarcomas affecting the young.

Molecular cancer therapeutics·2026

Related Experiment Video

Updated: Feb 8, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K

Clinker: visualizing fusion genes detected in RNA-seq data.

Breon M Schmidt1, Nadia M Davidson1,2, Anthony D K Hawkins1

  • 1Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington, Road, Parkville Vic 3052 Australia.

Gigascience
|July 9, 2018
PubMed
Summary

Clinker is a new bioinformatics tool that visualizes oncogenic fusion genes from RNA-sequencing data. This software aids researchers in interpreting complex gene fusions and their supporting evidence.

More Related Videos

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

394
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
06:22

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Published on: August 25, 2020

13.5K

Related Experiment Videos

Last Updated: Feb 8, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

394
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
06:22

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Published on: August 25, 2020

13.5K

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Genomic profiling reveals diverse oncogenic fusion genes.
  • Identifying fusion genes from RNA-sequencing (RNA-seq) data is established, but visualization remains a challenge.

Purpose of the Study:

  • To introduce Clinker, a bioinformatics tool for visualizing fusion genes.
  • To demonstrate Clinker's utility in interpreting RNA-seq data for fusion gene discovery.

Main Methods:

  • Clinker utilizes the superTranscript method.
  • The tool is implemented in Python, R, and Bpipe.
  • Clinker visualizes fusion genes and their supporting RNA-seq reads.

Main Results:

  • Clinker provides interpretable visualizations of RNA-seq data, facilitating fusion gene identification.
  • The tool was used to explore novel breakpoints in the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia.

Conclusions:

  • Clinker is a freely available software tool.
  • It enables effective visualization of fusion genes and the RNA-seq data crucial for their discovery.