ArticleBioinformatics (Oxford, England)2024
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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
41 citing papers in PubMed.
- Novel Thermophilic Species ofLife (Basel, Switzerland) · 2026Article
- Unveiling the Taxonomic Diversity and Unprecedented Biosynthetic Treasure of the Phylum Myxococcota.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A Modern Framework for Identifying Novel EnvironmentalLife (Basel, Switzerland) · 2026Article
- Article
- Physiology, functional genomics, and proteomics ofApplied and environmental microbiology · 2026Article
- Article
- Parasediminibacterium schistidii sp. nov., a novel member of the family Chitinophagaceae isolated from a glacier moss ball in the Canadian High Arctic.Antonie van Leeuwenhoek · 2026Article
- Aliikangiella litoralis sp. nov. and Aliikangiella aequoris sp. nov., isolated from coastal seawaters of the Yellow Sea.Journal of microbiology (Seoul, Korea) · 2026Article
- Taxonomic description of a novel genus,International journal of systematic and evolutionary microbiology · 2026Article
- Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.Current microbiology · 2026Article
- Draft metagenome-assembled genome sequence of aMicrobiology resource announcements · 2026Article
- Article
- ThreeViruses · 2026Article
- Enrichment and characterization of a haloalkaline-tolerant anammox bacterium.The ISME journal · 2026Article
- Article
- Resolving taxonomic uncertainties in the genusFrontiers in microbiology · 2026Article
- Reclassification of the genusInternational journal of systematic and evolutionary microbiology · 2026Article
- Microbial Evolution and Systematics: Archaea and Bacteria.Progress in molecular and subcellular biology · 2026Review
- Article
- Culture-independent discovery of a novel thermotolerant lipase and its producer from mesophilic anaerobic digestion sludge.Applied microbiology and biotechnology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summarySequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. AVAILABILITY AND IMPLEMENTATION: The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.