ArticlePeerJ2025
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu).
Article in PeerJ, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- Article
- Taxonomic description of a novel genus,International journal of systematic and evolutionary microbiology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.