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 <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 | ||
<strong>PRISM</strong>: http://grid.adapsyn.com/prism/#!/prism | <strong>PRISM</strong>: http://grid.adapsyn.com/prism/#!/prism | ||
*Reference: Skinnider, M.A. <em>et al, Nucleic Acids Res.</em> 2017 https://doi.org/10.1093/nar/gkx320 | *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, A.J. <em>et al, Nucleic Acids Res.</em> 2018 <strong>2</strong>;46 https://doi.org/10.1093/nar/gky383. | *Reference: Van Heel, A.J., <em>et al, Nucleic Acids Res.</em> 2018 <strong>2</strong>;46 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. <em>et al, J. Biotechnol.</em> 2009, <strong>140</strong>: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. <em>et al, Cell</em> 2014, <strong>158</strong>: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. <em>et al, Bioinformatics</em> 2015, <strong>32</strong>: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. <em>et al. Nucleic Acids Res.</em> 2017 https://doi.org/10.1093/nar/gkx360 | *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., <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 | ||
<strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/ | <strong>PKMiner</strong>: http://pks.kaist.ac.kr/pkminer/ | ||
*Reference: Kim J, Yi | *Reference: Kim, J., Yi, G.S., <em>BMC Microbiol.</em> 2012 <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 | ||
*Reference: Anand S et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340. | *Reference: Anand, S., <em>et al. Nucleic Acids Res.</em> 2010 ;38(Web Server issue):W487-96. 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 <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;<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 | ||
Revision as of 09:50, 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
- Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 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 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, G.S., BMC Microbiol. 2012 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 ;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 3;45 https://doi.org/10.1093/nar/gkx408.
RODEO: http://www.ripprodeo.org/manual.html
- Reference: Tietz, J. I., Nat Chem Biol. 2017;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
