Genome mining tools

From ActinoBase

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start

PRISM: http://grid.adapsyn.com/prism/#!/prism

BAGEL: http://bagel4.molgenrug.nl/

CLUSEAN: https://omictools.com/clusean-tool

ClusterFinder: https://github.com/petercim/ClusterFinder

  • Reference: Cimermancic, P., et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/

ARTS: https://arts3.ziemertlab.com/

2metDB: https://sourceforge.net/projects/secmetdb/

PKMiner: http://pks.kaist.ac.kr/pkminer/

SBSPKS: http://www.nii.ac.in/sbspks2.html

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php

RODEO: http://www.ripprodeo.org/manual.html

RiPPER: https://github.com/streptomyces/ripper

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki