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

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 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...

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

Organization of Genes

Organization of Genes

You might also read

Related Articles

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

Sort by

Same author

SHREC 2025: Protein surface shape retrieval including electrostatic potential.

Computers & graphics·2026

Same author

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX.

bioRxiv : the preprint server for biology·2026

Same author

Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.

bioRxiv : the preprint server for biology·2026

Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026

Same author

MVGFormer: Multi-view perspective with graph-guided transformer for cryo-ET segmentation.

Knowledge-based systems·2026

Same author

Peptide-protein docking: from physics-based models to generative intelligence.

Chemical communications (Cambridge, England)·2026

Search research articles

Related Experiment Video

Updated: Mar 6, 2026

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

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

Qing Wei¹, Ishita K Khan¹, Ziyun Ding²

¹Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.

BMC Bioinformatics

|March 22, 2017

Summary

NaviGO is a new web tool that analyzes and visualizes gene functions using Gene Ontology (GO) annotations. It quantifies functional similarity and associations, aiding in the interpretation of large genomics and proteomics datasets.

Keywords:

Function similarity GO GO annotation GO association score GO directed acyclic graph GO parental terms Gene function Gene function prediction Gene ontology Ontology function enrichment analysis

More Related Videos

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Related Experiment Videos

Last Updated: Mar 6, 2026

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

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Rapid growth in genomics and proteomics data necessitates efficient functional interpretation.
Gene Ontology (GO) is a standard vocabulary for gene function annotation.
Systematic analysis of GO annotations requires robust quantification and visualization tools.

Purpose of the Study:

To develop a web-based tool for analyzing and visualizing Gene Ontology (GO) function.
To quantify and visualize functional similarity and associations between GO terms and genes.

Main Methods:

Developed NaviGO, a web-based platform.
Implemented six different scoring methods for quantifying GO term and gene function similarity, including protein-protein interaction and context-based association scores.
Enabled interactive navigation and real-time visualization of functional groupings and statistical analysis of enriched functions.

Main Results:

NaviGO provides interactive visualization, retrieval, and computation of functional similarity and associations for GO terms and genes.
The tool quantifies similarity using multiple scores, including novel protein-protein interaction and context-based association measures.
Interactive exploration allows for intuitive understanding of functional relationships and identification of enriched functions.

Conclusions:

NaviGO is a novel web tool for visualizing and analyzing functional similarity and associations of GO terms and genes.
The tool facilitates the interpretation of large-scale functional genomics data.
NaviGO is freely accessible at http://kiharalab.org/web/navigo.