Genome mining tools

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

• Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
• Twitter: https://twitter.com/antiSMASH_dev

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

• Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

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

• Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

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

• Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7 https://doi.org/10.1016/j.jbiotec.2009.01.007

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

• Reference: Cimermancic, P., et al, Cell 2014, 158:412-21 https://doi.org/10.1016/j.cell.2014.06.034

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

• Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43 https://doi.org/10.1093/bioinformatics/btv713.

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

• Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

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

• Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3

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

• Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

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

• Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

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

• Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

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

• Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

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

• Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

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

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