ArticleNucleic acids research2013
BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 274 papers.
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Who cites it
274 citing papers in PubMed.
- Advances in tools, strategies, and applications of mining of microbial genomes for novel antimicrobials: a comprehensive review.Folia microbiologica · 2026Review
- Engineered antimicrobial-derived peptides to manipulate mixed microbial systems.Microbiology spectrum · 2026Article
- LanthMS: A Computational Tool for the Structure Elucidation of Lanthipeptides from Tandem Mass Spectrometry Data.Protein and peptide letters · 2026Article
- Dual-probe genome mining identifies citrulassin N, a novel citrulline modified lasso peptide fromFrontiers in microbiology · 2026Article
- Antifungal activity and genome annotation of Bacillus amyloliquefaciens subsp. plantarum SMLR1, a potential biocontrol agent of Rhizoctonia solani.World journal of microbiology & biotechnology · 2025Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Genomic and Metabolomic Insights into Metabolites of aMarine drugs · 2025Article
- A fast approach for structural and evolutionary analysis based on energetic profile protein comparison.Nature communications · 2025Article
- Direct Cloning and Heterologous Expression of the Dmxorosin Biosynthetic Gene Cluster fromInternational journal of molecular sciences · 2025Article
- Complete genome sequencing and probiotic characterization of promising lactic acid bacterial strains isolated from dairy products in Egyptian markets.BMC microbiology · 2025Article
- A gut-derivedmBio · 2025Article
- Bacteriocin prediction through cross-validation-based and hypergraph-based feature evaluation approaches.Frontiers in bioinformatics · 2025Article
- Review
- Comprehensive genomic analysis and evaluation of in vivo and in vitro safety of Heyndrickxia coagulans BC99.Scientific reports · 2024Article
- Preventing Fungal Spoilage from Raw Materials to Final Product: Innovative Preservation Techniques for Fruit Fillings.Foods (Basel, Switzerland) · 2024Review
- Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062.Probiotics and antimicrobial proteins · 2024Article
- Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain.Royal Society open science · 2024Article
- Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters.NAR genomics and bioinformatics · 2024Article
- Protein remote homology detection and structural alignment using deep learning.Nature biotechnology · 2024Article
- Bacteriocins: potentials and prospects in health and agrifood systems.Archives of microbiology · 2024Review
214 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying genes encoding bacteriocins and ribosomally synthesized and posttranslationally modified peptides (RiPPs) can be a challenging task. Especially those peptides that do not have strong homology to previously identified peptides can easily be overlooked. Extensive use of BAGEL2 and user feedback has led us to develop BAGEL3. BAGEL3 features genome mining of prokaryotes, which is largely independent of open reading frame (ORF) predictions and has been extended to cover more (novel) classes of posttranslationally modified peptides. BAGEL3 uses an identification approach that combines direct mining for the gene and indirect mining via context genes. Especially for heavily modified peptides like lanthipeptides, sactipeptides, glycocins and others, this genetic context harbors valuable information that is used for mining purposes. The bacteriocin and context protein databases have been updated and it is now easy for users to submit novel bacteriocins or RiPPs. The output has been simplified to allow user-friendly analysis of the results, in particular for large (meta-genomic) datasets. The genetic context of identified candidate genes is fully annotated. As input, BAGEL3 uses FASTA DNA sequences or folders containing multiple FASTA formatted files. BAGEL3 is freely accessible at http://bagel.molgenrug.nl.
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