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. 2018 Jul 2;46(W1):W278-W281.
doi: 10.1093/nar/gky383.

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

Auke J van Heel  1 , Anne de Jong  1 , Chunxu Song  1 , Jakob H Viel  1 , Jan Kok  1 , Oscar P Kuipers  1
Affiliations

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

Auke J van Heel et al. Nucleic Acids Res. .

Abstract

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

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Figures

Figure 1.
Figure 1.
General flow of the BAGEL4 web server. The left part is executed for all input DNA larger than a set threshold (default 3000 bp), the right part is executed for every detected area of interest (AOI).
Figure 2.
Figure 2.
Example graphics produced by BAGEL4. On the left top items can be turned on or off by clicking on the item. Genes are indicated as arrows and additional information is displayed (including a link to BLAST the protein) by mouse-over. The additional information disappears by clicking on the gene. Bottom (in blue), RNA expression data displayed in RPMK.
Figure 3.
Figure 3.
Example output of an alignment based on a BLAST hit with the core peptide database. The query is linked to a record (Nukacin A) in the core peptide database. Based on the UniProt identifier of the hit in the database, information available on modifications and bridging patterns is displayed. The leader peptide of the database record is highlighted in dark gray and modified residues are indicated with asterisks. Users should be aware that this information is only indicative for the query sequence.
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