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 <strong>1</strong>; 39
*Twitter: https://twitter.com/antiSMASH_dev
*Twitter: https://twitter.com/antiSMASH_dev


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<strong>BAGEL</strong>: http://bagel4.molgenrug.nl/
<strong>BAGEL</strong>: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J. <em>et al, Nucleic Acids Res.</em> 2018 Jul <strong>2</strong>;46  
*Reference: Van Heel, A.J. <em>et al, Nucleic Acids Res.</em> 2018 <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  
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<strong>SBSPKS</strong>: http://www.nii.ac.in/sbspks2.html
<strong>SBSPKS</strong>: http://www.nii.ac.in/sbspks2.html
*Reference: Anand S et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96.
*Reference: Anand S et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.  
*https://doi.org/10.1093/nar/gkq340.  


<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. <em>Nucleic Acids Res.</em> 2017 Jul <strong>3</strong>;45 https://doi.org/10.1093/nar/gkx408.
*Reference: Agrawal P. <em>Nucleic Acids Res.</em> 2017 <strong>3</strong>;45 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. I, <em>Nat Chem Biol.</em> 2017 May;<strong>13</strong>(5):470-478 https://doi.org/10.1038/nchembio.2319.
*Reference: Tietz J. I, <em>Nat Chem Biol.</em> 2017;<strong>13</strong>(5):470-478 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. <em>et al Nucleic Acids Res.</em>, 2019, <strong>47</strong>;(9):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


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


<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki
<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki

Revision as of 21:03, 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