ArticleNucleic acids research2025
Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Whole genome sequencing analysis and functional characterization of Lacticaseibacillus rhamnosus HP-B1083.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Tandem-sgRNA Provides an Effective Reverse Genetic Approach for Suppression of Streptomyces Biosynthetic Gene Clusters and Secondary Metabolism.ACS synthetic biology · 2026Article
- A guide to Direct Pathway Cloning (DiPaC) for natural product discovery.Essays in biochemistry · 2026Review
- Heterologous expression of NRPS and PKS pathways in Escherichia coli: from bottlenecks to biosynthetic platforms.Essays in biochemistry · 2026Review
- DiscERN: an automated genome mining tool for the discovery of evolutionarily related natural products.Nature communications · 2026Article
- AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.bioRxiv : the preprint server for biology · 2026Article
- Genome mining of amylases and amylase inhibitors fromMicrobial genomics · 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
- Streptomyces produce a diphtheria toxin-like exotoxin that targets insects.Nature microbiology · 2026Article
- Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions.bioRxiv : the preprint server for biology · 2026Article
- Synteny plot quality control with SyntenyQC.Bioinformatics (Oxford, England) · 2025Article
- Benchmarking methods for measuring biosynthetic gene cluster similarity and determination of gene cluster families.Bioinformatics (Oxford, England) · 2025Article
- CAGEcleaner: reducing genomic redundancy in gene cluster mining.Bioinformatics (Oxford, England) · 2025Article
- EquilibraTor streamlines molecular dynamics simulations in a single execution.Computational and structural biotechnology journal · 2025Article
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Abstract
Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and medicine. While various genome mining tools can identify and characterize gene clusters based on homology, they often overlook their evolutionary diversity, a crucial factor in revealing novel cluster functions and applications. To address this gap, we developed GATOR-GC, a targeted, homology-based genome mining tool that enables comprehensive and flexible exploration of gene clusters in a single execution. We show that GATOR-GC identified a diversity of over 4 million gene clusters similar to experimentally validated biosynthetic gene clusters (BGCs) that antiSMASH version 7 fails to detect. To highlight the utility of GATOR-GC, we identified previously uncharacterized co-occurring conserved genes potentially involved in mycosporine-like amino acid biosynthesis and mapped the taxonomic and evolutionary patterns of genomic islands that modify DNA with 7-deazapurines. Additionally, with its proximity-weighted similarity scoring, GATOR-GC successfully differentiated BGCs of the FK family of metabolites (e.g. rapamycin, FK506/520) according to their chemistries. When benchmarked on the FK-family of BGCs, GATOR-GC outperformed cblaster, zol, and fai. We anticipate GATOR-GC will be a valuable tool to assess gene cluster diversity for targeted, exploratory, and flexible genome mining.
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