Related Experiment Video
Updated: Jan 8, 2026
09:40
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
12.7K
VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses
Shahram Saghaei1, Malte Siemers2, Kilian L Ossetek1
1RNA Bioinformatics and High-Throughput Analysis, Faculty of Computer Science and Mathematics, Friedrich Schiller University Jena, Jena 07743, Germany.
Nucleic Acids Research
|December 17, 2025
Summary
VirJenDB centralizes virus sequence data from multiple sources, improving data reuse through community-driven curation and a user-friendly platform. This database enhances access to viral genomic and metadata for researchers.
Area of Science:
- Virology
- Bioinformatics
- Genomics
Background:
- High-throughput sequencing generates vast amounts of biological data, particularly viral sequences.
- Existing data repositories require extensive curation and quality control, posing challenges for data reuse due to data volume and repository multiplicity.
- Complexity in virus metadata curation hinders efficient data management and accessibility.
Purpose of the Study:
- To develop VirJenDB, a user-friendly platform for versioned, community-driven curation and ontology development of virus sequence data.
- To consolidate and standardize virus metadata from diverse sources, facilitating data accessibility and reuse.
- To create novel subsets of viral data, such as viral operational taxonomic units (vOTUs), for advanced downstream analyses.
Main Methods:
- Ingested virus sequences and associated metadata from 16 distinct sources, covering approximately 200 metadata fields.
- Implemented a community-driven curation process for up to 85 metadata fields, linking curated data to 15.4 million virus sequences.
- Generated a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences, preserving original sequences for variation analysis.
Main Results:
- VirJenDB integrates 15.4 million virus sequences, with 88% infecting eukaryotes and the remainder infecting prokaryotes.
- Significant progress in metadata curation, with up to 85 fields undergoing refinement and linked to the sequence data.
- A new vOTU dataset of 0.91 million sequences is available, alongside original sequences, enhancing comparative genomics and variation studies.
Conclusions:
- VirJenDB provides a centralized, curated resource to overcome challenges in virus data accessibility and reuse.
- The platform supports community-driven curation and ontology development, fostering collaborative research in virology.
- VirJenDB aims to bridge research communities by enabling meta-analyses, webtool integration, and metadata schema extensions for phages and eukaryotic viruses.
Related Concept Videos
01:29Viruses with RNA Genomes
730
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
730
01:26Size and Structure of Viral Genomes
622
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
622
01:29Viruses of Archaea
423
Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
423
01:28Introduction to Virus
1.1K
Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...
1.1K
00:50What are Viruses?
127.3K
Overview
127.3K
01:23The Antiviral System of Bacteria and Archaea: CRISPR
596
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this...
596