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BAGEL3 User Guide

BAGEL3 is very simple to use. The user can either select a genome present on the server from a dropdown menu or can upload a file from his computer. The required input is a folder or a file containing one or multiple DNA files in a FastA format. Also FastA files containing multiple DNA entries are allowed. If it is a folder it should be compressed into a zip rar or tar file.

 

Last Updated on Wednesday, 16 January 2013 14:45
 

Bacteriocin classification in BAGEL2

BAGEL2 predicts the class of putative bacteriocins it identifies. The (sub)classification scheme below is used. Subclasses of lantibiotics (class I) are as described by Willey et al. Subclasses of class II are as described by Cotter et al. Class III are large proteins.

Class I

A LanBC modified

B LanM modified

C lanM* modified

Class II


A Pediocin-like

B Two-component

C Cyclic peptides

D Miscellaneous

Class III

Large proteins

  1. Joanne M. Willey and Wilfred A. van der Donk, “Lantibiotics: Peptides of Diverse Structure and Function,” Annual Review of Microbiology 61, no. 1 (10, 2007): 477-501
  2. Paul D. Cotter, Colin Hill, and R. Paul Ross, “Bacteriocins: developing innate immunity for food,” Nat Rev Micro 3, no. 10 (October 2005): 777-788.