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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.3K
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.
19.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.2K
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...
6.2K

You might also read

Related Articles

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

Sort by
Same author

Comparison of Human Melanoma Single Cell Profiles to Evolutionary Medicine Model Xiphophorus Provides Insights in Disease Control.

Pigment cell & melanoma research·2026
Same author

Cave adaptation drives coordinated transcriptional remodeling across diverse cell types in the brain of a teleost fish.

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

Genomic and physiological changes in a sexually selected and frugivorous bird radiation.

Current biology : CB·2026
Same author

Strain-specific responses of avian influenza virus to disruption of solute carrier family 35 member A1 (SLC35A1) in chicken cells.

Poultry science·2026
Same author

Novel mechanisms of chemosensory adaptation to the cave environment.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Sep 16, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.9K

Agptools: a utility suite for editing genome assemblies.

Edward S Ricemeyer1,2, Rachel A Carroll1, Wesley C Warren1,3

  • 1Bond Life Sciences Center, University of Missouri, Columbia, MO 65221, United States.

Bioinformatics (Oxford, England)
|July 7, 2025
PubMed
Summary
This summary is machine-generated.

agptools is a new command-line software suite for editing AGP files, which describe genome assembly components. This tool addresses the lack of software for curating AGP files, enabling common operations like breaking, joining, and inverting sequences.

More Related Videos

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

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

Published on: May 22, 2018

9.3K
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

5.2K

Related Experiment Videos

Last Updated: Sep 16, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.9K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

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

Published on: May 22, 2018

9.3K
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

5.2K

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The AGP (Assembly/Annotation Gene Prediction) format is crucial for describing genome assembly structures, detailing how sequence components like contigs assemble into larger scaffolds or chromosomes.
  • Standard genome assembly submissions often include FASTA files for contig sequences and AGP files for assembly layout.
  • Existing genome assembly and scaffolding software can read and write AGP files, but tools for direct AGP file manipulation and curation are lacking.

Purpose of the Study:

  • To introduce agptools, a novel suite of command-line programs designed for the curation and manipulation of AGP files.
  • To provide essential functionalities for editing genome assembly layouts described in AGP format.
  • To offer an API for integrating AGP file handling into other bioinformatics software.

Main Methods:

  • Development of a Python-based command-line tool suite named agptools.
  • Implementation of core functionalities including breaking/joining sequences, inverting assembly components, assembling contigs based on AGP data, and coordinate system transformations.
  • Creation of an Application Programming Interface (API) for programmatic access to AGP file manipulation.

Main Results:

  • agptools provides a comprehensive solution for common AGP file editing tasks.
  • The software facilitates the assembly curation process by enabling direct manipulation of assembly layouts.
  • The included API allows for seamless integration of AGP handling into other bioinformatics pipelines.

Conclusions:

  • agptools fills a critical gap in bioinformatics software by providing dedicated tools for AGP file curation.
  • The suite enhances the efficiency and accuracy of genome assembly analysis and submission.
  • agptools is freely available, implemented in Python, and supports all major operating systems.