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.

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...

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....

You might also read

Related Articles

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

Sort by

Same author

What's past is prologue: epigenetic memory links transient inflammation to future disease.

Signal transduction and targeted therapy·2026

Same author

Urea-cycle control of fibroblast energetics after myocardial infarction.

Cardiovascular research·2026

Same author

Rezatapopt and the Return of Targetable p53.

MedComm·2026

Same author

Mechanism of Mutation in G Protein-Gated Inwardly Rectifying K<sup>+</sup> Channel in Familial Hyperaldosteronism-Type III: Residue Fluctuations and Conformational Instability.

Molecules (Basel, Switzerland)·2026

Same author

Human DNA methylation biomarkers in diabetic complications: from association to clinical translation.

Epigenomics·2026

Same author

Human islet amyloid polypeptide aggregation upregulates the mitochondrial cholesterol transport protein StAR and induces mitochondrial dysfunction in beta cells.

Diabetologia·2026

Search research articles

Related Experiment Video

Updated: Apr 20, 2026

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

Non-referenced genome assembly from epigenomic short-read data.

Antony Kaspi¹, Mark Ziemann, Samuel T Keating

¹a Epigenetics in Human Health and Disease Laboratory ; Baker IDI Heart and Diabetes Institute ; The Alfred Medical Research and Education Precinct ; Melbourne , Victoria , Australia ;

|December 2, 2014

Summary

This study introduces a novel computational pipeline for analyzing DNA methylation and chromatin modification using short-read sequencing data without needing a reference genome. The method enables efficient genome annotation and profiling, even for unreferenced species like Psammomys obesus.

Keywords:

ChIP-seq ChIP-seq, immunoprecipitated chromatin sequencing DMR, differentially methylated region DNA methylation High-throughput sequencing MBD-seq MBD-seq, methyl binding domain protein sequencing MeDIP-seq; methylated DNA immunoprecipitation sequencing Psammomys obesus RNA-seq, RNA sequencing de novo assembly epigenomic integration

More Related Videos

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Related Experiment Videos

Last Updated: Apr 20, 2026

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

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Area of Science:

Genomics
Bioinformatics
Epigenetics

Background:

Analyzing DNA methylation and chromatin modification typically requires a reference genome.
Existing computational methods are limited by the need for sequenced genomes.

Purpose of the Study:

To develop a reference-free computational pipeline for detecting DNA methylation and chromatin modification changes.
To enable analysis of epigenetic modifications in organisms lacking a reference genome.

Main Methods:

A de novo sequence assembly pipeline was developed using open-source software.
The pipeline performs sequence assembly, alignment, and differential enrichment measurement.
Methods were validated by comparing results with reference-based analyses.

Main Results:

The pipeline successfully detected DNA methylation and chromatin modification changes without a reference genome.
A strong correlation was observed between chromatin modification and gene expression.
The DNA methylation profile for the non-referenced Psammomys obesus genome was successfully constructed.

Conclusions:

This reference-free pipeline offers a powerful tool for epigenetic analysis in unsequenced or poorly annotated genomes.
The approach facilitates rapid annotation and visualization of genomic regions from short-read data.
It expands the scope of epigenetic research to a wider range of organisms.