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

5.8K
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...
5.8K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

836
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
836
Genomics02:02

Genomics

35.5K
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...
35.5K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
12.6K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

16.7K
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.
16.7K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

11.6K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
11.6K

You might also read

Related Articles

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

Sort by
Same author

Using Metabarcoding Techniques to Map Multiple Dung Beetle-Vertebrate iDNA Networks in a Southeast Asian Forest.

Molecular ecology resources·2026
Same author

Functional impact of genetic background on variable expressivity in neurodevelopmental disorders.

Nature communications·2026
Same author

A Dominant Founder Lineage Has Possible Fitness Costs for the Endangered Mexican Grey Wolf.

Molecular ecology·2026
Same author

Biallelic DAW1 variants reveal tissue-specific role in heterotaxy without primary ciliary dyskinesia.

Research square·2026
Same author

Patient-informed CRISPR screen identifies FLNB as a congenital heart disease and ciliopathy gene.

HGG advances·2026
Same author

Compound heterozygous DAW1 variants reveal tissue-specific roles in left-right patterning and congenital heart disease without primary ciliary dyskinesia.

medRxiv : the preprint server for health sciences·2026

Related Experiment Video

Updated: May 4, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

6.6K

Galaxy tools to study genome diversity.

Oscar C Bedoya-Reina, Aakrosh Ratan, Richard Burhans

  • 1Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA. webb@bx.psu.edu.

Gigascience
|January 1, 2014
PubMed
Summary
This summary is machine-generated.

Researchers developed user-friendly bioinformatics tools for analyzing genome-wide genetic variation in non-model organisms. These tools, accessible via the Galaxy web server, facilitate population genetics studies and ensure reproducible research for small labs studying species of interest.

More Related Videos

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

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

Published on: April 8, 2017

16.5K
G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

5.0K

Related Experiment Videos

Last Updated: May 4, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

6.6K
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

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

Published on: April 8, 2017

16.5K
G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

5.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Intra-species genetic variation analysis is crucial for understanding population structure, selection, and gene flow in vertebrates.
  • Decreasing genome sequencing costs enable small labs to generate full-genome variation data.
  • Limited access to and familiarity with computational tools hinder data analysis in these labs.

Purpose of the Study:

  • To provide a suite of user-friendly bioinformatics tools for analyzing nucleotide and amino-acid polymorphisms.
  • To make published genetic variation analyses reproducible.
  • To support genetic variation studies in non-model vertebrates and other organisms.

Main Methods:

  • Development of a tool suite for the Galaxy web server.
  • Handling of genetic polymorphisms from full-genome sequencing and SNP genotyping microarrays.
  • Application of tools to diverse datasets including vertebrate, fungal, human, and mitochondrial genomes.

Main Results:

  • A comprehensive tool collection for analyzing genetic variation data has been created.
  • The tools are designed for user-friendliness and reproducibility.
  • The utility of the tools is demonstrated across various biological contexts, including non-human vertebrates and fungi.

Conclusions:

  • A small team can successfully develop and distribute a Galaxy tool collection for a specific biological community.
  • The developed tools address the computational needs of biologists analyzing genetic variation data.
  • The project highlights the feasibility of creating accessible bioinformatics resources for research labs.