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.

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

You might also read

Related Articles

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

Sort by

Same author

Blunt-force assembly of programmable DNA architectures using π-π stacking.

Nature communications·2026

Same author

A PIWI protein-dependent DNA N6-adenine methylation pathway in <i>Oxytricha</i> protects genomic sequences from deletion.

bioRxiv : the preprint server for biology·2026

Same author

The R-loop grammar predicts R-loop formation under different topological constraints.

PLoS computational biology·2025

Same author

Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement.

Nucleic acids research·2025

Same author

Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement.

bioRxiv : the preprint server for biology·2025

Same author

Diversity and efficacy of insect sampling methods in an urban tropical dry forest of the Colombian Caribbean.

PeerJ·2025

Same journal

QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.

NAR genomics and bioinformatics·2026

Same journal

Correction to 'SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome'.

NAR genomics and bioinformatics·2026

Same journal

asms: finding allele-specific methylation in human genomes without phasing.

NAR genomics and bioinformatics·2026

Same journal

An epigenetic clock for chronological age estimation in East Asian populations.

NAR genomics and bioinformatics·2026

Same journal

The role of ATF4 in neurons under mitochondrial stress.

NAR genomics and bioinformatics·2026

Same journal

Distinct repeat architecture landscapes in the proteomes of protozoan parasites.

NAR genomics and bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 11, 2025

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Published on: November 1, 2014

SDRAP for annotating scrambled or rearranged genomes.

Jasper Braun^1,2, Rafik Neme^3,4, Yi Feng³

¹Department of Mathematics and Statistics, University of South Florida, Tampa, FL 33620, USA.

NAR Genomics and Bioinformatics

|November 9, 2023

Summary

This summary is machine-generated.

We developed a new software tool to analyze DNA rearrangements in scrambled genomes, improving genome annotation accuracy for complex genetic data.

More Related Videos

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: Jul 11, 2025

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

Published on: November 1, 2014

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Large-scale genome rearrangements occur in various organisms.
Ciliates provide a unique model system for studying programmed genome rearrangements due to their highly scrambled genomes.
Existing genome annotation methods are insufficient for analyzing complex genomic rearrangements.

Purpose of the Study:

To present a theoretical framework and software for analyzing DNA rearrangement annotations.
To enable systematic extraction and analysis of rearrangements from precursor and product genome assemblies.
To address the limitations of current annotation methods for highly rearranged genomes.

Main Methods:

Developed a theoretical framework for DNA rearrangement analysis.
Implemented a software tool for systematic extraction and analysis of rearrangement annotations.
Utilized pairs of genome assemblies (precursor and product versions) for analysis.

Main Results:

Achieved more complete precursor-product mappings compared to previous methods.
The software makes no assumptions about rearrangement structures, offering flexibility.
The approach allows for full transparency and reproducibility in analysis.

Conclusions:

The developed software provides a robust solution for annotating highly scrambled genomes.
This method enhances the analysis of DNA rearrangements in model systems like ciliates.
The adaptable software can be applied to diverse genomic datasets from various sources.