Genome mining tools - Revision history

Nelly at 23:52, 17 November 2021

2021-11-17T23:52:13Z

← Older revision		Revision as of 23:52, 17 November 2021
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	*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.		*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

	[https://github.com/medema-group/bigslice BiG SLiCE]:<sup>15</sup>		[https://github.com/medema-group/bigslice <strong>BiG SLiCE </strong>]:<sup>15</sup>
	*Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.		*Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.

Nelly at 23:51, 17 November 2021

2021-11-17T23:51:36Z

← Older revision		Revision as of 23:51, 17 November 2021
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	*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.		*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

	[https://github.com/medema-group/bigslice BiG SLiCE]		[https://github.com/medema-group/bigslice BiG SLiCE]:<sup>15</sup>
	* Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.		*Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.


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	# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. <em>Nat Chem Biol</em> 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9		# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. <em>Nat Chem Biol</em> 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
	# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> https://doi.org/10.1099/mgen.0.000260		# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> https://doi.org/10.1099/mgen.0.000260
	e
	# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, <em>GigaScience</em>, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154		# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, <em>GigaScience</em>, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154

Nelly at 23:50, 17 November 2021

2021-11-17T23:50:43Z

← Older revision		Revision as of 23:50, 17 November 2021
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	*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.		*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.

			[https://github.com/medema-group/bigslice BiG SLiCE]
			* Allows identification of cross-species BGC patterns. This is a specialized Big data method that avoids network comparison to allow the classification of millions of BGCs.


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	# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. <em>Nat Chem Biol</em> 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9		# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. <em>Nat Chem Biol</em> 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
	# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> https://doi.org/10.1099/mgen.0.000260		# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> https://doi.org/10.1099/mgen.0.000260
			e
			# Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema (2021) BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, <em>GigaScience</em>, Volume 10, Issue 1, giaa154, https://doi.org/10.1093/gigascience/giaa154

Nelly: addin big scpae reference and CORASON description

2021-11-17T20:17:53Z

addin big scpae reference and CORASON description

← Older revision		Revision as of 20:17, 17 November 2021
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	*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.		*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

	[https://~~omictools~~.~~com~~/~~big-scape-tool~~ <strong>BiG-SCAPE</strong>]:<sup>13</sup>		[https://bigscape-corason.secondarymetabolites.org/<strong>BiG-SCAPE</strong>]:<sup>13</sup>
	*Identification of gene ~~clusters~~ families		*Identification of gene cluster families through a collection of genomes. This software classifies antiSMASH outputs into cluster families. Also on this paper, software CORASON searches any gene cluster in a set of genomes.

	[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</strong>]:<sup>14</sup>		[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</strong>]:<sup>14</sup>
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	# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. <em>Nature Chemical Biology</em>, 13(5):470-478 doi: 10.1038/nchembio.2319.		# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. <em>Nature Chemical Biology</em>, 13(5):470-478 doi: 10.1038/nchembio.2319.
	# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192		# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
	# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> ~~2019 .~~ https://doi.org/10.1099/mgen.0.000260		# Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. (2020) A computational framework to explore large-scale biosynthetic diversity. <em>Nat Chem Biol</em> 16, 60–68. https://doi.org/10.1038/s41589-019-0400-9
			# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. (2019) EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> https://doi.org/10.1099/mgen.0.000260

Nelly at 19:45, 17 November 2021

2021-11-17T19:45:11Z

Sam Prudence at 09:00, 3 June 2021

2021-06-03T09:00:17Z

← Older revision		Revision as of 09:00, 3 June 2021
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	[https://github.com/streptomyces/ripper <strong>RiPPER</strong>]:<sup>12</sup>		[https://github.com/streptomyces/ripper <strong>RiPPER</strong>]:<sup>12</sup>
	*Identification of RiPP precursor peptides and biosynthetic gene clusters		*Identification of RiPP precursor peptides and biosynthetic gene clusters
			*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

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

Alicia at 13:28, 16 August 2019

2019-08-16T13:28:42Z

← Older revision		Revision as of 13:28, 16 August 2019
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	Some useful genome mining resources are listed below:		Some useful genome mining resources are listed below:

	<strong>antiSMASH</strong>:<sup>1</sup> ~~https://antismash.secondarymetabolites.org/#!/start~~		[https://antismash.secondarymetabolites.org/#!/start <strong>antiSMASH</strong>]:<sup>1</sup> (antibiotics and Secondary Metabolite Analysis Shell)
	*~~Twitter:~~ https://twitter.com/antiSMASH_dev		*Identification and annotation of secondary metabolite gene clusters
			*[https://twitter.com/antiSMASH_dev Twitter]

	<strong>PRISM</strong>:<sup>2</sup> ~~http://grid.adapsyn.com/prism/#!/prism~~		[http://grid.adapsyn.com/prism/#!/prism <strong>PRISM</strong>]:<sup>2</sup> (PRediction Informatics for Secondary Metabolism)
			*Identification of nonribosomal peptides, type I and II polyketides and RiPPs

	<strong>BAGEL</strong>:<sup>3</sup> ~~http://bagel4.molgenrug.nl/~~		[http://bagel4.molgenrug.nl/ <strong>BAGEL</strong>]:<sup>3</sup>
			* Identification of gene clusters for bacteriocins and RiPPs

	<strong>CLUSEAN</strong>:<sup>4</sup> ~~https://omictools.com/clusean-tool~~		[https://omictools.com/clusean-tool <strong>CLUSEAN</strong>]:<sup>4</sup>
			*Annotation and analysis of secondary metabolite gene clusters

	<strong>ClusterFinder</strong>:<sup>5</sup> ~~https://github.com/petercim/ClusterFinder~~		[https://github.com/petercim/ClusterFinder <strong>ClusterFinder</strong>]:<sup>5</sup>
			*Identification of secondary metabolite gene clusters

	<strong>~~CASSIS~~</strong>:<sup>6</sup> ~~https://sbi.hki-jena.de/cassis/~~		[https://arts3.ziemertlab.com/ <strong>ARTS</strong>]:<sup>6</sup> (Antibiotic Resistant Target Seeker)
			*Genome mining for secondary metabolites and potential antibiotics based on antibiotic resistance targets

	<strong>~~ARTS~~</strong>:<sup>7</sup> ~~https://arts3.ziemertlab.com/~~		[https://sourceforge.net/projects/secmetdb/ <strong>2metDB</strong>]:<sup>7</sup>
			*Genome mining for polyketides and nonribosomal peptides

	<strong>~~2metDB~~</strong>:<sup>8</sup> ~~https://sourceforge.net/projects/secmetdb/~~		[http://pks.kaist.ac.kr/pkminer/ <strong>PKMiner</strong>]:<sup>8</sup>
			*Genome mining for type II polyketide synthases

	<strong>~~PKMiner~~</strong>:<sup>9</sup> ~~http://pks.kaist.ac.kr/pkminer/~~		[http://www.nii.ac.in/sbspks2.html <strong>SBSPKS</strong>]:<sup>9</sup>
			*Sequence analysis of polyketide synthases

	<strong>~~SBSPKS~~</strong>:<sup>10</sup> ~~http://www.nii.ac.in/sbspks2.html~~		[http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php <strong>RiPPMINER</strong>]:<sup>10</sup>
			*Genome mining and deciphering chemical structures of RiPPs

	<strong>~~RiPPMINER~~</strong>:<sup>11</sup> ~~http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php~~		[http://www.ripprodeo.org/manual.html <strong>RODEO</strong>]:<sup>11</sup> (Rapid ORF Description and Evaluation Online)
			*Identification of biosynthetic gene clusters and prediction of RiPP precursor peptides

	<strong>~~RODEO~~</strong>:<sup>12</sup> ~~http://www.ripprodeo.org/manual.html~~		[https://github.com/streptomyces/ripper <strong>RiPPER</strong>]:<sup>12</sup>
			*Identification of RiPP precursor peptides and biosynthetic gene clusters

	~~<strong>RiPPER</strong>:<sup>13</sup>~~ https://~~github~~.com/~~streptomyces~~/~~ripper~~		[https://omictools.com/big-scape-tool <strong>BiG-SCAPE</strong>]

	~~<strong>BiG-SCAPE</strong>:~~ https://~~omictools~~.com/~~big-scape-tool~~		[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</strong>]

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

	# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. <em>Nucleic Acids Research</em>, 1; 39 doi: 10.1093/nar/gkr466		# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. <em>Nucleic Acids Research</em>, 1; 39 doi: 10.1093/nar/gkr466
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	# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. <em>Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007		# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. <em>Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
	# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) <em>Cell</em>, 158:412-21 doi: 10.1016/j.cell.2014.06.034		# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) <em>Cell</em>, 158:412-21 doi: 10.1016/j.cell.2014.06.034
	# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. <em>Bioinformatics</em>, 32:1138-43 doi: 10.1093/bioinformatics/btv713.
	# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. <em>Nucleic Acids Research</em>, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360		# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. <em>Nucleic Acids Research</em>, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
	# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. <em>Methods in Enzymology</em>, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3		# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. <em>Methods in Enzymology</em>, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3

Alicia at 10:53, 16 August 2019

2019-08-16T10:53:26Z

Alicia at 10:49, 16 August 2019

2019-08-16T10:49:24Z

Alicia at 10:38, 16 August 2019

2019-08-16T10:38:21Z

← Older revision		Revision as of 19:45, 17 November 2021
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	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.		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 uncharacterized biosynthetic gene clusters (BGCs) for natural products.

	Some useful genome mining resources are listed below:		Some useful genome mining resources are listed below:
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	*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.		*Click [https://www.springer.com/gp/book/9781071613573 here] for a RiPPER user guide (chapter 14) or email Dr Andy Truman (Andrew.truman@jic.ac.uk) to request a copy.

	[https://omictools.com/big-scape-tool <strong>BiG-SCAPE</strong>]		[https://omictools.com/big-scape-tool <strong>BiG-SCAPE</strong>]:<sup>13</sup>
			*Identification of gene clusters families

			[https://github.com/nselem/EvoMining/wiki <strong>EvoMining</strong>]:<sup>14</sup>
			*Identification of expansions of gene families from central metabolism that have been recruited into biosynthetic gene clusters.


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

	# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. <em>Nucleic Acids Research</em>, 1; 39 doi: 10.1093/nar/gkr466		# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. <em>Nucleic Acids Research</em>, 1; 39 doi: 10.1093/nar/gkr466
	# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. <em>et al, Nucleic Acids Research</em>, doi: 10.1093/nar/gkx320		# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. <em>et al, Nucleic Acids Research</em>, doi: 10.1093/nar/gkx320
	# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly ~~web server~~ to thoroughly mine RiPPs and bacteriocins. <em>Nucleic Acids Research</em>, 2;46 doi: org/10.1093/nar/gky383.		# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly webserver to thoroughly mine RiPPs and bacteriocins. <em>Nucleic Acids Research</em>, 2;46 doi: org/10.1093/nar/gky383.
	# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. <em>Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007		# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. <em>Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
	# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) <em>Cell</em>, 158:412-21 doi: 10.1016/j.cell.2014.06.034		# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) <em>Cell</em>, 158:412-21 doi: 10.1016/j.cell.2014.06.034
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	# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. <em>Methods in Enzymology</em>, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3		# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. <em>Methods in Enzymology</em>, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
	# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. <em>BMC Microbiology</em>, 8;12:169. doi: 10.1186/1471-2180-12-169.		# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. <em>BMC Microbiology</em>, 8;12:169. doi: 10.1186/1471-2180-12-169.
	# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases. <em>Nucleic Acids Research</em>, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.		# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure-based sequence analysis of polyketide synthases. <em>Nucleic Acids Research</em>, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
	# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. <em>Nucleic Acids Research</em>, 3;45 doi: 10.1093/nar/gkx408.		# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. <em>Nucleic Acids Research</em>, 3;45 doi: 10.1093/nar/gkx408.
	# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. <em>Nature Chemical Biology</em>, 13(5):470-478 doi: 10.1038/nchembio.2319.		# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. <em>Nature Chemical Biology</em>, 13(5):470-478 doi: 10.1038/nchembio.2319.
	# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192		# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192
			# Nelly Sélem-Mojica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero, Fancisco Barona-Gómez. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. <em>Microbial Genomics </em> 2019 . https://doi.org/10.1099/mgen.0.000260

← Older revision		Revision as of 10:53, 16 August 2019
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	<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki		<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki

	# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences <em>Nucleic Acids Research</em> 1; 39 doi: 10.1093/nar/gkr466		# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. <em>Nucleic Acids Research</em>, 1; 39 doi: 10.1093/nar/gkr466
	# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes <em>et al, Nucleic Acids Research</em> doi: 10.1093/nar/gkx320		# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. <em>et al, Nucleic Acids Research</em>, doi: 10.1093/nar/gkx320
	# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins <em>Nucleic Acids Research</em> 2;46 doi: org/10.1093/nar/gky383.		# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. <em>Nucleic Acids Research</em>, 2;46 doi: org/10.1093/nar/gky383.
	# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters<em>~~et al,~~ Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007		# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. <em>Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
	# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters (2014) <em>~~et al,~~ Cell</em> 158:412-21 doi: 10.1016/j.cell.2014.06.034		# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014) <em>Cell</em>, 158:412-21 doi: 10.1016/j.cell.2014.06.034
	# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes <em>Bioinformatics</em>, 32:1138-43 doi: 10.1093/bioinformatics/btv713.		# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. <em>Bioinformatics</em>, 32:1138-43 doi: 10.1093/bioinformatics/btv713.
	# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery <em> Nucleic Acids Research</em> doi: 10.1093/nar/gkx360		# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. <em>Nucleic Acids Research</em>, 3;45(W1):W42-W48 doi: 10.1093/nar/gkx360
	# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data <em>Methods in Enzymology </em> 458:181-217 doi: 10.1016/S0076-6879(09)04808-3		# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. <em>Methods in Enzymology</em>, 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
	# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases <em>BMC Microbiology </em> 8;12:169. doi: 10.1186/1471-2180-12-169.		# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. <em>BMC Microbiology</em>, 8;12:169. doi: 10.1186/1471-2180-12-169.
	# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases <em>Nucleic Acids Research</em> ;38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.		# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases. <em>Nucleic Acids Research</em>, 38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
	# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links <em>Nucleic Acids Research</em> 3;45 doi: 10.1093/nar/gkx408.		# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. <em>Nucleic Acids Research</em>, 3;45 doi: 10.1093/nar/gkx408.
	# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape <em>Nature Chemical Biology</em> 13(5):470-478 doi: 10.1038/nchembio.2319.		# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape. <em>Nature Chemical Biology</em>, 13(5):470-478 doi: 10.1038/nchembio.2319.
	# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192		# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192

← Older revision		Revision as of 10:49, 16 August 2019
Line 34:		Line 34:
	<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki		<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki

	# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences <em>Nucleic Acids Research</em~~> <strong~~>1~~</strong>~~; 39 doi: 10.1093/nar/gkr466		# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences <em>Nucleic Acids Research</em> 1; 39 doi: 10.1093/nar/gkr466
	# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes <em>et al, Nucleic Acids Research</em> doi: 10.1093/nar/gkx320		# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes <em>et al, Nucleic Acids Research</em> doi: 10.1093/nar/gkx320
	# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins <em>Nucleic Acids Research</em~~> <strong~~>2~~</strong>~~;46 doi: org/10.1093/nar/gky383.		# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins <em>Nucleic Acids Research</em> 2;46 doi: org/10.1093/nar/gky383.
	# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters<em>et al, Journal of Biotechnology</em>, ~~<strong>~~140~~</strong>~~:13-7 doi: 10.1016/j.jbiotec.2009.01.007		# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters<em>et al, Journal of Biotechnology</em>, 140:13-7 doi: 10.1016/j.jbiotec.2009.01.007
	# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters (2014) <em>et al, Cell</em~~> <strong~~>158~~</strong>~~:412-21 doi: 10.1016/j.cell.2014.06.034		# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters (2014) <em>et al, Cell</em> 158:412-21 doi: 10.1016/j.cell.2014.06.034
	# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes <em>Bioinformatics</em>, ~~<strong>~~32~~</strong>~~:1138-43 doi: 10.1093/bioinformatics/btv713.		# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes <em>Bioinformatics</em>, 32:1138-43 doi: 10.1093/bioinformatics/btv713.
	# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery <em> Nucleic Acids Research</em> doi: 10.1093/nar/gkx360		# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery <em> Nucleic Acids Research</em> doi: 10.1093/nar/gkx360
	# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data <em>Methods in Enzymology </em~~> <strong~~>458~~</strong>~~:181-217 doi: 10.1016/S0076-6879(09)04808-3		# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data <em>Methods in Enzymology </em> 458:181-217 doi: 10.1016/S0076-6879(09)04808-3
	# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases <em>BMC Microbiology </em~~> <strong~~>8~~</strong>~~;12:169. doi: 10.1186/1471-2180-12-169.		# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases <em>BMC Microbiology </em> 8;12:169. doi: 10.1186/1471-2180-12-169.
	# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases <em>Nucleic Acids Research</em> ;38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.		# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases <em>Nucleic Acids Research</em> ;38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
	# Agrawal, P., <em>Nucleic Acids ~~Res.~~</em~~> 2017 <strong~~>3~~</strong>~~;45 doi: 10.1093/nar/gkx408.		# Agrawal, P., Khater, S., Gupta, M., Sain, N., Mohanty, D. (2017) RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links <em>Nucleic Acids Research</em> 3;45 doi: 10.1093/nar/gkx408.
	# Tietz, J. I., <em>~~Nat Chem Biol.~~</em~~> 2017;<strong~~>13~~</strong>~~(5):470-478 doi: 10.1038/nchembio.2319.		# Tietz, J. I., Schwalen, C.J., Patel, P.S., Maxson, T., Blair, P.M., Tai, H.C., Zakai, U.I., Mitchell, D.A. (2017) A new genome-mining tool redefines the lasso peptide biosynthetic landscape <em>Nature Chemical Biology</em> 13(5):470-478 doi: 10.1038/nchembio.2319.
	# Santos-Aberturas, J. <em>~~et al~~ Nucleic Acids Research</em>, ~~2019, <strong>~~47~~</strong>~~;(9):4624–4637 doi: 10.1093/nar/gkz192		# Santos-Aberturas, J., Chandra, G., Frattaruolo, L., Lacret, R., Pham, T. H., Vior, N. M., Eyles, T. H., Truman, A. W. (2019) Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool <em>Nucleic Acids Research</em>, 47;(9):4624–4637 doi: 10.1093/nar/gkz192

← Older revision		Revision as of 10:38, 16 August 2019
Line 34:		Line 34:
	<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki		<strong>EvoMining</strong>: https://github.com/nselem/EvoMining/wiki

	#1. Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences <em>Nucleic Acids Research</em> <strong>1</strong>; 39 doi: 10.1093/nar/gkr466		# Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E., Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences <em>Nucleic Acids Research</em> <strong>1</strong>; 39 doi: 10.1093/nar/gkr466
	#2. Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes <em>et al, Nucleic Acids Research</em> doi: 10.1093/nar/gkx320		# Skinnider, M.A., Merwin, N. J., Johnston, C. W., Magarvey, N. A. (2017) PRISM 3: expanded prediction of natural product chemical structures from microbial genomes <em>et al, Nucleic Acids Research</em> doi: 10.1093/nar/gkx320
	#3. Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins <em>Nucleic Acids Research</em> <strong>2</strong>;46 doi: org/10.1093/nar/gky383.		# Van Heel, A.J., de Jong, A., Song, C., Viel, J. H., Kok, J., Kuipers, O. P. (2018) BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins <em>Nucleic Acids Research</em> <strong>2</strong>;46 doi: org/10.1093/nar/gky383.
	#4. Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters<em>et al, Journal of Biotechnology</em>, <strong>140</strong>:13-7 doi: 10.1016/j.jbiotec.2009.01.007		# Weber, T., Rausch, C., Lopez, P., Hoof, I., Gaykova, V., Huson, D. H., Wohlleben, W. (2009) CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters<em>et al, Journal of Biotechnology</em>, <strong>140</strong>:13-7 doi: 10.1016/j.jbiotec.2009.01.007
	#5. Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters (2014) <em>et al, Cell</em> <strong>158</strong>:412-21 doi: 10.1016/j.cell.2014.06.034		# Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., Birren, B.W., Takano, E., Sali, A., Linington, R.G., Fischbach, M.A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters (2014) <em>et al, Cell</em> <strong>158</strong>:412-21 doi: 10.1016/j.cell.2014.06.034
	#6. Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes <em>Bioinformatics</em>, <strong>32</strong>:1138-43 doi: 10.1093/bioinformatics/btv713.		# Wolf, T., Shelest, V., Nath, N., Shelest, E. (2015) CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes <em>Bioinformatics</em>, <strong>32</strong>:1138-43 doi: 10.1093/bioinformatics/btv713.
	#7. Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery <em> Nucleic Acids Research</em> doi: 10.1093/nar/gkx360		# Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B., Ziemert, N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery <em> Nucleic Acids Research</em> doi: 10.1093/nar/gkx360
	#8. Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data <em>Methods in Enzymology </em> <strong>458</strong>:181-217 doi: 10.1016/S0076-6879(09)04808-3		# Bachmann, B. O., and Ravel, J., (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data <em>Methods in Enzymology </em> <strong>458</strong>:181-217 doi: 10.1016/S0076-6879(09)04808-3
	#9. Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases <em>BMC Microbiology </em> <strong>8</strong>;12:169. doi: 10.1186/1471-2180-12-169.		# Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases <em>BMC Microbiology </em> <strong>8</strong>;12:169. doi: 10.1186/1471-2180-12-169.
	#~~10.~~ Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases <em>Nucleic Acids Research</em> ;38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.		# Anand, S., Prasad, M.V., Yadav, G., Kumar, N., Shehara, J., Ansari, M.Z., Mohanty, D. (2010) SBSPKS: structure based sequence analysis of polyketide synthases <em>Nucleic Acids Research</em> ;38(Web Server issue):W487-96. doi: 10.1093/nar/gkq340.
	#~~11.~~ Agrawal, P., <em>Nucleic Acids Res.</em> 2017 <strong>3</strong>;45 doi: 10.1093/nar/gkx408.		# Agrawal, P., <em>Nucleic Acids Res.</em> 2017 <strong>3</strong>;45 doi: 10.1093/nar/gkx408.
	#~~12.~~ Tietz, J. I., <em>Nat Chem Biol.</em> 2017;<strong>13</strong>(5):470-478 doi: 10.1038/nchembio.2319.		# Tietz, J. I., <em>Nat Chem Biol.</em> 2017;<strong>13</strong>(5):470-478 doi: 10.1038/nchembio.2319.
	#~~13.~~ Santos-Aberturas, J. <em>et al Nucleic Acids Research</em>, 2019, <strong>47</strong>;(9):4624–4637 doi: 10.1093/nar/gkz192		# Santos-Aberturas, J. <em>et al Nucleic Acids Research</em>, 2019, <strong>47</strong>;(9):4624–4637 doi: 10.1093/nar/gkz192