Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome Annotation and Assembly

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.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

RNA-seq

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...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Alternative RNA Splicing

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 Splicing

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...

You might also read

Related Articles

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

Sort by

Same author

Confusion between firearms and electrical weapons as a factor in police shootings.

Forensic science, medicine, and pathology·2022

Same author

Physicochemical Properties of Starch Isolated from Bracken (Pteridium aquilinim) Rhizome.

Journal of food science·2015

Same author

Chip Scale Atomic Resonator Frequency Stabilization System With Ultra-Low Power Consumption for Optoelectronic Oscillators.

IEEE transactions on ultrasonics, ferroelectrics, and frequency control·2015

Same author

Topological Superfluid and Majorana Zero Modes in Synthetic Dimension.

Scientific reports·2015

Same author

Prodrug AST-003 Improves the Therapeutic Index of the Multi-Targeted Tyrosine Kinase Inhibitor Sunitinib.

PloS one·2015

Same author

Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient.

Scientific reports·2015

Same journal

Genetic analysis of imaging-derived phenotypes.

Nature reviews. Genetics·2026

Same journal

Genetic origins and constraints of evolutionary innovation.

Nature reviews. Genetics·2026

Same journal

Single-cell four-omics with CHARM.

Nature reviews. Genetics·2026

Same journal

Molecular integration of seasonal temperature signals in flowering time control.

Nature reviews. Genetics·2026

Same journal

RBPscan measures protein-RNA interactions in living cells.

Nature reviews. Genetics·2026

Same journal

Revisiting retinal and macular degeneration in the genomics era.

Nature reviews. Genetics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 29, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Next-generation transcriptome assembly.

Jeffrey A Martin¹, Zhong Wang

¹Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA. jamartin@lbl.gov

Nature Reviews. Genetics

|September 8, 2011

Summary

This summary is machine-generated.

Transcriptome assembly from RNA sequencing (RNA-seq) data is crucial for understanding gene expression. This review covers new methods for transcriptome assembly, addressing challenges with short reads and incomplete references.

More Related Videos

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

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

Published on: May 9, 2017

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Related Experiment Videos

Last Updated: May 29, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

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

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

Published on: May 9, 2017

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Transcriptomics studies often use incomplete reference transcriptomes, missing full transcript catalogs and variations.
Deep RNA sequencing (RNA-seq) and advanced algorithms enable whole transcriptome reconstruction, even without a reference genome.

Purpose of the Study:

To review recent advancements in transcriptome assembly approaches.
To discuss challenges and future perspectives in transcriptome assembly.

Main Methods:

Summarizes reference-based transcriptome assembly strategies.
Details de novo transcriptome assembly approaches.
Explores combined reference-based and de novo strategies.

Main Results:

Highlights the impact of sequencing technologies and assembly algorithms on transcriptome reconstruction.
Identifies informatics challenges associated with assembling billions of short RNA-seq reads.
Presents an overview of current transcriptome assembly methodologies.

Conclusions:

Transcriptome assembly is evolving with new technologies and algorithms.
Addressing challenges in handling large, short-read datasets is key for future progress.
Comprehensive transcriptome assembly is vital for accurate biological insights.