BAGEL4

So you are interested to know what the antimicrobial potential is of your DNA. Welcome to the longest running bacteriocin and RiPP mining web server.

Input: BAGEL4 is simple to use, all you have to do is upload your DNA in fasta format. Multiple entries per file are allowed. File size maximum is 50 Mb larger datasets can be used for this please contact us. Also please be aware that reads smaller than 3000 bp are ignored so uploading them is not very useful. These type of settings can be adapted, if you have a specific request concerning settings please contact us. Expression data can be added optionally. This should be done in de so called bedgraph format

Output: After the run has finished you will end up at an overview table displaying all the detected clusters. AOI= area of interest. These are potential clusters responsible for the production of RiPPs and other bacteriocins.

Example output graphic from BAGEL4

Elements listed in the top left can be clicked to show or hide them. Including so called small ORFs. Small ORFs can be helpful in the manual evaluation of the cluster when no core peptide was detected by the software. Example output graphic from BAGEL4 Core peptide Blast:

The core peptide blast returns an output table with an alignment. The leader peptide is highlighted in dark grey and cystein and lanthionine bridges are indicated in the bridge line(s). Additional links to background information is available. Context based detection of clusters is based on the table below.

RiPP classIdentification rule
Lanthipeptide_class_II PF05147 AND PF13575
Lanthipeptide_class_I PF05147 AND PF04738|PF14028
LAPs PF02624 AND PF00881
Bottromycin PF04055 AND PF02624
Sactipeptides PF04055 AND Sac_1
Glyocin TIGR04195 AND PF03412
Head_to_tail_cyclized_peptide PF01944 AND PF00005
Thiopeptide PF14028 AND PF02624 AND PF00881
Microcin PF02794
Lasso_peptide PF13471
Lanthipeptide_class_III labKC
Cyanobactin CyaG Linaridin LinL
This table originates from the BAGEL3 publication