Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

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...
Next-generation Sequencing03:00

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.
RNA-seq03:21

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 microarray-based...
Genome Annotation and Assembly03:36

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.
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Genome Size and the Evolution of New Genes03:21

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.

You might also read

Related Articles

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

Sort by
Same author

Make the Unhearable Visible: Exploring Visualization for Musical Instrument Practice.

IEEE transactions on visualization and computer graphics·2026
Same author

RSVP for VPSA : A Meta Design Study on Rapid Suggestive Visualization Prototyping for Visual Parameter Space Analysis.

IEEE transactions on visualization and computer graphics·2024
Same author

Beware of Validation by Eye: Visual Validation of Linear Trends in Scatterplots.

IEEE transactions on visualization and computer graphics·2024
Same author

Human-Robot Collaboration With a Corrective Shared Controlled Robot in a Sanding Task.

Human factors·2024
Same author

<i>IsoBayes</i>: a Bayesian approach for single-isoform proteomics inference.

bioRxiv : the preprint server for biology·2024
Same author

A Problem Space for Designing Visualizations.

IEEE computer graphics and applications·2023
Same journal

MesoSplats: Texture Synthesis with Gaussian Splatting.

IEEE transactions on visualization and computer graphics·2026
Same journal

GLLA: A Unified Force-Directed Graph Layout Framework Supporting Local Adjustments.

IEEE transactions on visualization and computer graphics·2026
Same journal

Multi-Perception Crowd: Learning to combine entity and implicit perception for diverse crowd simulation.

IEEE transactions on visualization and computer graphics·2026
Same journal

Hiding in Plain Sight: Camouflaging Real-world Objects.

IEEE transactions on visualization and computer graphics·2026
Same journal

RTF2Mesh: Restricted Tangent Face Based Mesh Compression With Neural Displacement Fields.

IEEE transactions on visualization and computer graphics·2026
Same journal

Practical Occluder Generation for Mobile Games.

IEEE transactions on visualization and computer graphics·2026
See all related articles

Related Experiment Video

Updated: May 28, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Sequence Surveyor: leveraging overview for scalable genomic alignment visualization.

Danielle Albers1, Colin Dewey, Michael Gleicher

  • 1University of Wisconsin-Madison, USA. dalbers@cs.wisc.edu

IEEE Transactions on Visualization and Computer Graphics
|October 29, 2011
PubMed
Summary
This summary is machine-generated.

New visualization tools help researchers understand large-scale genome alignments. Sequence Surveyor uses perceptual science and signal processing to display patterns in over 100 bacterial genomes.

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Related Experiment Videos

Last Updated: May 28, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Area of Science:

  • Bioinformatics
  • Data Visualization
  • Genomics

Background:

  • Genome alignment visualization is crucial for understanding genomic data.
  • Increasing sequencing data necessitates scalable visualization tools.
  • Current tools struggle to handle large-scale multiple genome alignments.

Purpose of the Study:

  • To introduce overview visualization tools for large-scale multiple genome alignment data.
  • To design visualizations that elucidate large-scale patterns in massive genomic datasets.
  • To present Sequence Surveyor, a prototype for scalable whole-genome alignment visualization.

Main Methods:

  • Utilizing perceptual science, signal processing theory, and generality for scalable visualization design.
  • Developing Sequence Surveyor, which visualizes sequences in parallel using variable color, position, and aggregation encodings.
  • Applying perceptual science to ensure visual manageability at scale and signal processing for aggregation schemes.

Main Results:

  • Demonstrated visualization techniques that remain visually manageable for large datasets.
  • Showcased aggregation schemes that highlight global trends, outliers, and data distributions.
  • Successfully visualized alignments with over 100 whole bacterial genomes.

Conclusions:

  • Overview visualization tools are essential for managing and interpreting large-scale genomic data.
  • Sequence Surveyor effectively visualizes complex multiple whole-genome alignments.
  • The presented framework enables scalable visualization beyond current approaches, aiding genomic research.