ArticleBriefings in bioinformatics2024
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- InJournal of bacteriology · 2026Article
- InbioRxiv : the preprint server for biology · 2026Article
- GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.Nucleic acids research · 2026Article
- Identification and characterization of botulinum neurotoxin-like two-component toxins inScience advances · 2025Article
- Repeatability of protein structural evolution following convergent gene fusions.Nature communications · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- A widespread accessory protein family diversifies the effector repertoire of the type VI secretion system spike.Nature communications · 2024Article
- Function and mechanism of action of the small regulatory RNA ArcZ inRNA (New York, N.Y.) · 2024Review
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
9 authors.
Funding
Abstract
The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across large genomic databases or user-generated datasets remains a challenge. Here, we introduce AnnoView, a web server designed for interactive exploration of gene neighborhoods across the bacterial and archaeal tree of life. Our server offers users the ability to identify, compare, and visualize gene neighborhoods of interest from 30 238 bacterial genomes and 1672 archaeal genomes, through integration with the comprehensive Genome Taxonomy Database and AnnoTree databases. Identified gene neighborhoods can be visualized using pre-computed functional annotations from different sources such as KEGG, Pfam and TIGRFAM, or clustered based on similarity. Alternatively, users can upload and explore their own custom genomic datasets in GBK, GFF or CSV format, or use AnnoView as a genome browser for relatively small genomes (e.g. viruses and plasmids). Ultimately, we anticipate that AnnoView will catalyze biological discovery by enabling user-friendly search, comparison, and visualization of genomic data. AnnoView is available at http://annoview.uwaterloo.ca.
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Registered trials
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.