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.

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Evolution of Microbial Genome

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

You might also read

Related Articles

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

Sort by

Same author

Functional characterization of Pseudomonas soli VMAP1 as a biocontrol agent against Xanthomonas vesicatoria in tomato plants.

Scientific reports·2026

Same author

Type VI-secretion system-mediated competition and virulence in clinical and environmental <i>Stenotrophomonas maltophilia</i>.

Microbiology spectrum·2026

Same author

CAMP: a modular metagenomics analysis system for integrated multistep data exploration.

NAR genomics and bioinformatics·2026

Same author

Genomic characterization of Staphylococcus epidermidis Se252 isolated from the rhizosphere of a Brazilian endemic plant.

BMC genomics·2025

Same author

Comparison of Morbidity and Mortality Rates following Endovascular Repair of Complex Abdominal and Thoraco-abdominal Aortic Aneurysms by Self-identified Race and Ethnicity in the Vascular Quality Initiative.

European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery·2025

Same author

BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.

Nucleic acids research·2025

Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026

Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 26, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

The Genome Reverse Compiler: an explorative annotation tool.

Andrew S Warren¹, João Carlos Setubal

¹Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA. anwarren@vt.edu

BMC Bioinformatics

|January 29, 2009

Summary

This summary is machine-generated.

The Genome Reverse Compiler (GRC) is a new, open-source tool simplifying whole genome annotation for researchers. It offers an automated, user-friendly solution, reducing the complexity of gene characterization in biological research.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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: Jun 26, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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:

Genomics
Bioinformatics
Molecular Biology

Background:

Decreasing sequencing costs make whole genome sequencing integral to research.
Existing gene annotation tools are not user-friendly for daily biological research.
Most annotation pipelines are institutional services or complex, hard-to-maintain systems.

Purpose of the Study:

To develop an automated, user-friendly whole genome annotation tool.
To address the limitations of current gene characterization methods.
To provide an accessible solution for life science researchers and bioinformaticians.

Main Methods:

Developed the Genome Reverse Compiler (GRC), an open-source, automated annotation tool.
GRC requires only a Linux operating system, avoiding complex third-party software installations.
Evaluated GRC performance on prokaryotic groups using its built-in comparison module.

Main Results:

GRC is an easy-to-use, automated annotation tool.
It is independent of third-party software, requiring only a Linux OS.
GRC performance was evaluated on prokaryotes, demonstrating its capability.

Conclusions:

GRC simplifies whole genome annotation, eliminating the need for complex pipeline setup or online services.
Users only need to provide the genome and function resource files.
GRC offers high usability and a minimal learning curve, filling a niche for explorative whole-genome annotation.