BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

By A. J. Heel, Anne de Jong, Manuel Montalbán-López, Jan Kok, Oscar P. Kuipers. Nucleic Acids Res., 2013

466 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/5f6e4865438e3e0f120fe5da27ec0da7f5f85b83

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In Molecular Biology

1. Oscar P. Kuipers
2. Manuel Montalbán-López
3. Patricia Alvarez-Sieiro
4. Anne de Jong
5. Jan Kok
6. Dongdong Mu

Citations in the corpus

• Bacteriocins of lactic acid bacteria: extending the family (2016, methodology): “Diverse tools have been created that can be used for the automated screening of bacteriocin gene clusters (Blin et al. 2013; van Heel et al. 2013).”
• BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins (2018, methodology): “The database includes the prokaryotic part of the uniref90 database extended with the context protein database used by BAGEL3 (19).”