ArticleBioinformatics advances2025
Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Anaerobic riboflavin degradation by human gutJournal of bacteriology · 2026Article
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Carbon monoxide dehydrogenase-encoding microorganisms in volcanic astrobiological analogues: an enzyme system to investigate the evolution of life.FEMS microbiology ecology · 2026Review
- Anaerobic riboflavin degradation by human gutbioRxiv : the preprint server for biology · 2026Article
- Symbiosis reshapes metabolism of sulfate-reducing bacteria in gutless marine worms.The ISME journal · 2026Article
- Genomic evidence for aerotrophy as a defining trait of Ktedonobacteria inhabiting silica-rich oligotrophic caves.ISME communications · 2026Article
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- GlobDB: a comprehensive species-dereplicated microbial genome resource.Bioinformatics advances · 2025Article
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Authors and funding
6 authors.
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Abstract
Motivation: Gene function annotation in microbial genomes and metagenomes is a fundamental Results: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Availability and implementation: Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.
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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.