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

16.8K
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.
16.8K
Plant Breeding and Biotechnology01:59

Plant Breeding and Biotechnology

17.2K
Crop cultivation has a long history in human civilization, with records showing the cultivation of cereal plants beginning at around 8000 BC. This early plant breeding was developed primarily to provide a steady supply of food.
17.2K
Genomics02:02

Genomics

35.6K
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...
35.6K
Microbe-Plant Interactions01:09

Microbe-Plant Interactions

155
Microbe-plant interactions represent a dynamic spectrum of associations shaped by intricate chemical signaling. These interactions can be neutral, beneficial, or detrimental, and profoundly influence plant physiology, growth, and ecosystem function. The plant microbiome, comprising bacteria, fungi, archaea, protists, and viruses, plays a pivotal role in mediating these effects through surface colonization, internal colonization, or systemic symbiosis.Mutualistic associations, particularly with...
155
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.7K
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...
12.7K
Synthetic Biology02:55

Synthetic Biology

4.4K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
4.4K

You might also read

Related Articles

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

Sort by
Same author

Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.

Rice (New York, N.Y.)·2026
Same author

Genomic insights into the medieval cultivation history of influential high-yielding Asian rice.

Scientific reports·2026
Same author

Off-target sequence variations driven by the intrinsic properties of the Cas-sgRNA-DNA complex in genome editing.

PloS one·2025
Same author

S-540956, a CpG Oligonucleotide Annealed to a Complementary Strand With an Amphiphilic Chain Unit, Acts as a Potent Cancer Vaccine Adjuvant by Targeting Draining Lymph Nodes.

Frontiers in immunology·2022
Same author

Development of an SSR marker-based genetic linkage map and identification of a QTL associated with flowering time in <i>Eustoma</i>.

Breeding science·2021
Same author

Simultaneous induction of mutant alleles of two allergenic genes in soybean by using site-directed mutagenesis.

BMC plant biology·2020

Related Experiment Video

Updated: May 5, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

23.1K

MEGANTE: a web-based system for integrated plant genome annotation.

Hisataka Numa1, Takeshi Itoh

  • 1Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.

Plant & Cell Physiology
|November 21, 2013
PubMed
Summary

MEGANTE simplifies plant genome annotation for researchers without bioinformatics expertise. This web-based system automates sequence analysis, ORF prediction, and functional annotation for 24 plant species.

Keywords:
Gene predictionPlant genome annotationWeb service

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

9.8K
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

9.9K

Related Experiment Videos

Last Updated: May 5, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

23.1K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

9.8K
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

9.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • High-throughput sequencing generates vast genomic data requiring large-scale annotation.
  • Genome annotation is essential for data analysis but demands significant bioinformatics expertise.
  • Existing tools often have complex configurations, limiting accessibility for non-specialists.

Purpose of the Study:

  • To develop an accessible web-based system for plant genome annotation.
  • To provide a user-friendly platform for researchers lacking bioinformatics skills.
  • To automate and integrate multiple annotation steps for efficient genome analysis.

Main Methods:

  • MEGANTE is a web-based system requiring only sequence upload and species selection.
  • It automatically executes multiple analysis programs for exon-intron structure prediction and ORF identification.
  • Functional annotation includes similarity and domain searches against known protein databases.
  • Results are visualized using GBrowse and downloadable in Excel format.

Main Results:

  • MEGANTE successfully predicts exon-intron structures and ORFs for plant genomic sequences.
  • Functional annotation provides insights into the roles of predicted ORFs.
  • The system supports 24 plant species and sequences up to 10 Mb.
  • User data is stored server-side for persistent access.

Conclusions:

  • MEGANTE significantly lowers the barrier to plant genome annotation.
  • It empowers researchers to perform complex analyses without extensive bioinformatics training.
  • The system facilitates efficient and accessible plant genome research.