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 Jul 1; 39
• Twitter: https://twitter.com/antiSMASH_dev

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

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

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

• Reference: Van Heel AJ Nucleic Acids Res. 2018 Jul 2;46(W1):W278-W281.
• https://doi.org/10.1093/nar/gky383.

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

• Reference: Weber, T., et al., 2009, J. Biotechnol. 140:13-7

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

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

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

• Reference: Wolf, T., et al., 2015, Bioinformatics 32:1138-43

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

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

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

• Reference: Bachmann, B. O. and Ravel, J., 2009, Methods Enzymol. 458:181-217

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

• Reference: Kim J, Yi GS BMC Microbiol. 2012 Aug 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 Jul;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 Jul 3;45(W1):W80-W88.
• https://doi.org/10.1093/nar/gkx408.

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

• Reference: Tietz J INat Chem Biol. 2017 May;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 Research, Volume 47, Issue 9, 21 May 2019, Pages 4624–4637
• https://doi.org/10.1093/nar/gkz192

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

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