Genome mining tools: Difference between revisions

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<strong>2metDB</strong>: https://sourceforge.net/projects/secmetdb/  
<strong>2metDB</strong>: https://sourceforge.net/projects/secmetdb/  
*Reference: Bachmann, B. O., and Ravel, J., <em>Methods Enzymol.</em> 2009 <strong>458</strong>:181-217
*Reference: Bachmann, B. O., and Ravel, J., <em>Methods Enzymol.</em> 2009 <strong>458</strong>:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3


<strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/  
<strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/  

Revision as of 09:55, 10 June 2019

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

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

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

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

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

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

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