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 | *Reference: Skinnider, M.A. <em>et al, Nucleic Acids Res.</em> 2017 https://doi.org/10.1093/nar/gkx320 | ||
<strong>BAGEL</strong>: http://bagel4.molgenrug.nl/ | <strong>BAGEL</strong>: http://bagel4.molgenrug.nl/ | ||
*Reference: Van Heel | *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. | *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. | *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. | *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. | *Reference: Alanjary, M. <em>et al. Nucleic Acids Res.</em> 2017 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., | *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. | ||
<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 | *Reference: Agrawal P. <em>Nucleic Acids Res.</em> 2017 Jul <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 | *Reference: Tietz J. I, <em>Nat Chem Biol.</em> 2017 May;<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. et al Nucleic Acids | *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
- 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 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 Jul 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
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/
- 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
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 https://doi.org/10.1093/nar/gkx408.
RODEO: http://www.ripprodeo.org/manual.html
- Reference: Tietz J. I, Nat 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 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