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

Rapid Identification of Pathogens01:25

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

You might also read

Related Articles

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

Sort by
Same author

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT.

bioRxiv : the preprint server for biology·2026
Same author

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.

Nature microbiology·2025
Same author

Automated annotation and validation of human respiratory virus sequences using VADR.

Database : the journal of biological databases and curation·2025
Same author

Automated Annotation and Validation of Human Respiratory Virus Sequences using VADR.

bioRxiv : the preprint server for biology·2025
Same author

Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.

Environmental microbiome·2025
Same author

Expansion of the tmRNA sequence database and new tools for search and visualization.

NAR genomics and bioinformatics·2025

Related Experiment Video

Updated: Jul 9, 2026

Avian Influenza Surveillance with FTA Cards: Field Methods, Biosafety, and Transportation Issues Solved
12:09

Avian Influenza Surveillance with FTA Cards: Field Methods, Biosafety, and Transportation Issues Solved

Published on: August 2, 2011

19.2K

Influenza sequence validation and annotation using VADR.

Vincent C Calhoun1, Eneida L Hatcher1, Linda Yankie1

  • 1National Center for Biotechnology Information, U.S. National Library of Medicine, National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, MD 20894, United States.

Database : the Journal of Biological Databases and Curation
|September 19, 2024
PubMed
Summary

Viral Annotation DefineR (VADR) now annotates influenza sequences, offering improved accuracy and broader subtype coverage compared to the existing FLu ANnotation tool (FLAN). This standalone software is now available for public use.

More Related Videos

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
08:46

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

10.5K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.1K

Related Experiment Videos

Last Updated: Jul 9, 2026

Avian Influenza Surveillance with FTA Cards: Field Methods, Biosafety, and Transportation Issues Solved
12:09

Avian Influenza Surveillance with FTA Cards: Field Methods, Biosafety, and Transportation Issues Solved

Published on: August 2, 2011

19.2K
Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
08:46

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

10.5K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.1K

Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • GenBank receives tens of thousands of influenza sequences annually.
  • The FLu ANnotation tool (FLAN) has validated and annotated influenza sequences since 2007 but is only available as a webserver.
  • Viral Annotation DefineR (VADR) is a standalone tool used by GenBank for other viral sequences.

Purpose of the Study:

  • To adapt and validate Viral Annotation DefineR (VADR) for accurate influenza sequence annotation.
  • To provide a standalone, improved alternative to the FLu ANnotation tool (FLAN).

Main Methods:

  • Developed VADR influenza models using FLAN reference sequences.
  • Adapted VADR software for influenza sequence processing.
  • Compared VADR annotation results with FLAN on influenza sequences.

Main Results:

  • VADR and FLAN showed consistent results for most influenza sequences.
  • VADR demonstrated higher accuracy than FLAN in cases of disagreement.
  • VADR successfully annotated influenza D and novel influenza A subtypes (H17-H19, N10-N11) that FLAN could not process.

Conclusions:

  • VADR provides accurate and comprehensive annotation for a wide range of influenza sequences.
  • VADR is a superior standalone alternative to FLAN for influenza sequence analysis.
  • VADR 1.6.3 and its influenza models are publicly available for download.