ArticleViruses2024
VOGDB-Database of Virus Orthologous Groups.
Article in Viruses, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.Applied and environmental microbiology · 2026Article
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- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Review
- Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.Communications biology · 2026Article
- Elucidating the protein interaction network of one of the largest icosahedral capsids in the virosphere.The EMBO journal · 2026Article
- Article
- AliFilter: a machine learning approach to alignment filtering.Molecular biology and evolution · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Intrinsic dataset features drive mutational effect prediction by protein language models.bioRxiv : the preprint server for biology · 2026Article
- Article
- Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.bioRxiv : the preprint server for biology · 2026Article
- A Unified Framework to Prioritize RNA Virus Cross-Species Transmission Risk Across an Expansive Host Landscape.Viruses · 2026Article
- Identification and comparative genomic analysis of prophage sequences and CRISPR‒Cas immunity in Methylococcus genomes: insights into industrial methane bioconversion.Biotechnology for biofuels and bioproducts · 2026Article
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
- Host life-history strategy is a critical determinant of virulent phage infection propensity.The ISME journal · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- Dispersal pathways and infection strategies within the Global Halophilic Virome.ISME communications · 2026Article
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Authors and funding
10 authors.
Funding
Abstract
Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up to date as for many cellular genomes. To tackle these problems, we have developed VOGDB, which is a database of virus orthologous groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote similarity. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments, and the third layer uses predicted protein structures to find the most remote similarity. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGD B uses all virus genomes from RefSeq and partially reannotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is the inclusion of both prokaryotic and eukaryotic viruses in the same clustering process, which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at vogdb.org under the CC BY 4.0 license.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.