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.

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cis-regulatory Sequences

Cis-regulatory Sequences

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...

Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

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

Sort by

Same author

The howler monkey genome provides new insights into the distinctive howling and folivorous adaptations of New World monkeys.

Genome biology·2026

Same author

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2.

bioRxiv : the preprint server for biology·2026

Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026

Same author

The genomic basis of independent marine transitions in turtles: convergent episodic adaptation and demographic shifts.

Molecular biology and evolution·2026

Same author

Chromosome-level genome assembly of the common tenrec, Tenrec ecaudatus (Schreber, 1778), a new model for early placental mammal evolution.

BMC genomics·2026

Same author

Learning genes deeply.

Nature methods·2026

Search research articles

Related Experiment Video

Updated: Mar 23, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

Virag Sharma¹, Anas Elghafari², Michael Hiller³

¹Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.

Nucleic Acids Research

|March 27, 2016

Summary

We developed CESAR (Coding Exon-Structure Aware Realigner) to accurately identify conserved coding exons in genomes. This tool overcomes limitations in existing alignments, improving gene annotation across species.

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

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Related Experiment Videos

Last Updated: Mar 23, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

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

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Area of Science:

Genomics
Comparative genomics
Bioinformatics

Background:

Accurate identification of coding genes is crucial for genome annotation.
Existing whole genome alignments often contain spurious frameshifts and splice site errors in conserved exons.
These errors hinder effective mapping of gene annotations across genomes.

Purpose of the Study:

To develop a novel method for accurate detection and realignment of conserved coding exons.
To overcome limitations of spurious frameshifts and splice site mutations in whole genome alignments.
To improve comparative gene annotation across diverse vertebrate genomes.

Main Methods:

Developed CESAR (Coding Exon-Structure Aware Realigner) to realign coding exons.
Incorporated reading frame and splice site information into the realignment process.
Applied CESAR to human gene annotations for comparative analysis in 99 vertebrate genomes.

Main Results:

CESAR effectively avoids spurious frameshifts in conserved genes.
The tool detects 91% of shifted splice sites and identifies thousands of additional conserved exons.
99% of exons without inactivating mutations identified by CESAR match real exons.

Conclusions:

CESAR significantly enhances the accuracy of coding exon identification and gene annotation.
The developed method provides a valuable resource for comparative genomics and gene annotation.
CESAR is applicable to various alignments for accurate coding gene annotation in diverse genomes.