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Related Concept Videos

RNA Splicing01:32

RNA Splicing

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...
RNA Splicing01:32

RNA Splicing

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...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: RNA Splicing

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...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
RNA-seq03:21

RNA-seq

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 microarray-based...

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Related Experiment Video

Updated: Jun 24, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

TopHat: discovering splice junctions with RNA-Seq.

Cole Trapnell1, Lior Pachter, Steven L Salzberg

  • 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. cole@cs.umd.edu

Bioinformatics (Oxford, England)
|March 18, 2009
PubMed
Summary

TopHat is a new algorithm for RNA-Seq data that identifies novel gene splice junctions without prior knowledge. This efficient tool significantly speeds up RNA-Seq analysis, enabling faster gene expression studies.

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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

Related Experiment Videos

Last Updated: Jun 24, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • RNA-Seq generates millions of short sequence reads for gene expression analysis.
  • Existing alignment software requires known splice junctions, limiting novel splice variant discovery.
  • TopHat is a novel algorithm for mapping RNA-Seq reads without relying on known splice sites.

Purpose of the Study:

  • To develop an efficient read-mapping algorithm for RNA-Seq data.
  • To identify novel splice junctions from RNA-Seq reads.
  • To improve the speed and capabilities of RNA-Seq data analysis.

Main Methods:

  • Developed TopHat, an efficient read-mapping algorithm.
  • Applied TopHat to mammalian RNA-Seq data.
  • Benchmarked TopHat's performance against existing methods.

Main Results:

  • TopHat identified over 72% of known splice junctions and nearly 20,000 novel junctions.
  • The TopHat pipeline maps 2.2 million reads per CPU hour, processing an entire experiment in under a day.
  • Identified challenges in de novo splice site discovery from RNA-Seq data.

Conclusions:

  • TopHat enables efficient and comprehensive splice junction discovery from RNA-Seq data.
  • The algorithm significantly accelerates RNA-Seq analysis.
  • Further algorithm development is needed for ab initio splice site discovery.