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Related Concept Videos

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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 primer.
Since the...

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Related Experiment Video

Updated: Jun 2, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Manfred G Grabherr1, Brian J Haas, Moran Yassour

  • 1Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.

Nature Biotechnology
|May 17, 2011
PubMed
Summary
This summary is machine-generated.

Trinity enables de novo transcriptome assembly for any organism, reconstructing full-length transcripts without a reference genome. This method accurately identifies alternatively spliced and duplicated genes, improving transcript discovery.

More Related Videos

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Related Experiment Videos

Last Updated: Jun 2, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Massively parallel sequencing provides deep transcriptomic data.
  • Current transcriptome reconstruction methods often require a reference genome.
  • This limits transcript assembly in organisms lacking genomic resources.

Purpose of the Study:

  • To develop a de novo transcriptome assembly method (Trinity).
  • To enable full-length transcript reconstruction without a reference genome.
  • To evaluate Trinity's performance on diverse species.

Main Methods:

  • Utilized de Bruijn graphs for efficient assembly.
  • Developed the Trinity software for de novo transcriptome assembly.
  • Tested on fission yeast, mouse, and whitefly transcriptomic data.

Main Results:

  • Trinity successfully reconstructed a large fraction of full-length transcripts.
  • Identified alternatively spliced isoforms and transcripts from duplicated genes.
  • Outperformed other de novo assemblers in recovering full-length transcripts across expression levels.

Conclusions:

  • Trinity offers a unified solution for transcriptome reconstruction.
  • Enables accurate transcript assembly even with missing or partial reference genomes.
  • Significantly advances transcriptomic studies in non-model organisms.