Genome mining tools: Difference between revisions

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<strong>antiSMASH</strong>: https://antismash.secondarymetabolites.org/#!/start  
<strong>antiSMASH</strong>: https://antismash.secondarymetabolites.org/#!/start  
*Reference: Medema, M.H. <em>et al Nucleic Acids Res.</em> 2011 Jul <strong>1</strong>; 39
*Reference: Medema, M.H. <em>et al, Nucleic Acids Res.</em> 2011 Jul <strong>1</strong>; 39
*Twitter: https://twitter.com/antiSMASH_dev
*Twitter: https://twitter.com/antiSMASH_dev


<strong>PRISM</strong>: http://grid.adapsyn.com/prism/#!/prism  
<strong>PRISM</strong>: http://grid.adapsyn.com/prism/#!/prism  
*Reference: Skinnider, M.A. et al, Nucleic Acids Research 2017  
*Reference: Skinnider, M.A. <em>et al, Nucleic Acids Res.</em> 2017 https://doi.org/10.1093/nar/gkx320
*https://doi.org/10.1093/nar/gkx320


<strong>BAGEL</strong>: http://bagel4.molgenrug.nl/
<strong>BAGEL</strong>: http://bagel4.molgenrug.nl/
*Reference: Van Heel AJ Nucleic Acids Res. 2018 Jul 2;46(W1):W278-W281.
*Reference: Van Heel, A.J. <em>et al, Nucleic Acids Res.</em> 2018 Jul <strong>2</strong>;46  
*https://doi.org/10.1093/nar/gky383.
*https://doi.org/10.1093/nar/gky383.


<strong>CLUSEAN</strong>: https://omictools.com/clusean-tool  
<strong>CLUSEAN</strong>: https://omictools.com/clusean-tool  
*Reference: Weber, T., et al., 2009, J. Biotechnol. 140:13-7
*Reference: Weber, T. <em>et al, J. Biotechnol.</em> 2009, <strong>140</strong>:13-7


<strong>ClusterFinder</strong>: https://github.com/petercim/ClusterFinder
<strong>ClusterFinder</strong>: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al., 2014, Cell 158:412-21  
*Reference: Cimermancic, P. <em>et al, Cell</em> 2014, <strong>158</strong>:412-21  


<strong>CASSIS</strong>: https://sbi.hki-jena.de/cassis/  
<strong>CASSIS</strong>: https://sbi.hki-jena.de/cassis/  
*Reference: Wolf, T., et al., 2015, Bioinformatics 32:1138-43
*Reference: Wolf, T. <em>et al, Bioinformatics</em> 2015, <strong>32</strong>:1138-43


<strong>ARTS</strong>: https://arts3.ziemertlab.com/  
<strong>ARTS</strong>: https://arts3.ziemertlab.com/  
*Reference: Alanjary, M., et al., 2017, Nucleic Acids Res.  
*Reference: Alanjary, M. <em>et al. Nucleic Acids Res.</em> 2017 https://doi.org/10.1093/nar/gkx360
*https://doi.org/10.1093/nar/gkx360


<strong>2metDB</strong>: https://sourceforge.net/projects/secmetdb/  
<strong>2metDB</strong>: https://sourceforge.net/projects/secmetdb/  
*Reference: Bachmann, B. O. and Ravel, J., 2009, Methods Enzymol. 458:181-217
*Reference: Bachmann, B. O. and Ravel, J., <em>Methods Enzymol.</em> 2009 <strong>458</strong>:181-217


<strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/  
<strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/  
*Reference: Kim J, Yi GS BMC Microbiol. 2012 Aug 8;12:169.  
*Reference: Kim J, Yi GS <em>BMC Microbiol.</em> 2012 Aug <strong>8</strong>;12:169. https://doi.org/10.1186/1471-2180-12-169.
*https://doi.org/10.1186/1471-2180-12-169.


<strong>SBSPKS</strong>: http://www.nii.ac.in/sbspks2.html
<strong>SBSPKS</strong>: http://www.nii.ac.in/sbspks2.html
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<strong>RiPPMINER</strong>: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php  
<strong>RiPPMINER</strong>: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php  
*Reference: Agrawal P Nucleic Acids Res. 2017 Jul 3;45(W1):W80-W88.
*Reference: Agrawal P. <em>Nucleic Acids Res.</em> 2017 Jul <strong>3</strong>;45 https://doi.org/10.1093/nar/gkx408.
*https://doi.org/10.1093/nar/gkx408.


<strong>RODEO</strong>: http://www.ripprodeo.org/manual.html  
<strong>RODEO</strong>: http://www.ripprodeo.org/manual.html  
*Reference: Tietz J INat Chem Biol. 2017 May;13(5):470-478.
*Reference: Tietz J. I, <em>Nat Chem Biol.</em> 2017 May;<strong>13</strong>(5):470-478 https://doi.org/10.1038/nchembio.2319.
*https://doi.org/10.1038/nchembio.2319.


<strong>RiPPER</strong>: https://github.com/streptomyces/ripper  
<strong>RiPPER</strong>: https://github.com/streptomyces/ripper  
*Reference: Santos-Aberturas, J. et al Nucleic Acids Research, Volume 47, Issue 9, 21 May 2019, Pages 4624–4637
*Reference: Santos-Aberturas, J. <em>et al Nucleic Acids Res.</em>, 2019, <strong>47</strong>;(9):4624–4637
*https://doi.org/10.1093/nar/gkz192
*https://doi.org/10.1093/nar/gkz192



Revision as of 21:01, 8 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/

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

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