ArticleBMC bioinformatics2023
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 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
103 citing papers in PubMed, 130 citations in OpenAlex.
- Genetic and enzymatic basis of xylooligosaccharide metabolism byGut microbes · 2026Article
- Structural insights and therapeutic targets in Acinetobacter baumannii capsule biosynthesis.FEBS letters · 2026Article
- Members of theMicrobial genomics · 2026Article
- Genome mining guided identification of new furo[3,2-c]pyridones phaeopyridones A-C from the endophytic fungus Phaeobotryon negundinis 12020.Natural products and bioprospecting · 2026Article
- Biosynthetic diversity and antifungal potential of soil-derivedApplied and environmental microbiology · 2026Article
- Identification of Siderophores With Unexpected Antibacterial Properties From Actinoplanes teichomyceticus.Chembiochem : a European journal of chemical biology · 2026Article
- Unveiling the Taxonomic Diversity and Unprecedented Biosynthetic Treasure of the Phylum Myxococcota.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic insights into specialized and primary metabolism gene clusters in methicillin-resistant Staphylococcus aureus from Egyptian community settings.BMC genomics · 2026Article
- Comparative genomics and methylome profiling ofMicrobial genomics · 2026Article
- Phylogenetic and Functional Analysis of β-Glucanases in Tannerella forsythia Reveals Distinct GH16 Family Glycoside Hydrolase Lineages in Oral Bacteria.Research square · 2026Article
- Mining the Galium aparine L. microbiome: genome-guided discovery and experimental validation of metallophore-producing endophytic bacteria.BMC genomics · 2026Article
- Article
- Synergistic Bactericidal Effects of R- and F-Type Pyocin Cocktails Against ClinicalAntibiotics (Basel, Switzerland) · 2026Article
- Article
- Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.Microbiology spectrum · 2026Article
- In Vivo Characterization of theJournal of fungi (Basel, Switzerland) · 2026Article
- Biosynthesis, Structure, and Antibiotic Properties of Gelatinamin A, a Triculamin-Like Lasso Peptide.Chembiochem : a European journal of chemical biology · 2026Article
- The interplay of specialized metabolites, antibiotic resistance, and virulence in Enterococcus faecium: in silico analysis of bacterial genomes.BMC genomics · 2026Article
- Genome Mining-Guided Discovery of the Glycosylated Griseorhodin Congener Ruskamycin.Journal of natural products · 2026Article
- BisCEET: A Visual Browser for Biosynthetic Gene Clusters Aiding in the Identification of Natural Product Variants and Distinct Tailoring Enzymes.Journal of natural products · 2026Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundCo-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret.
resultsThe comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query.
conclusionOverall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl .
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.