antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Tilmann Weber,Kai Blin,Srikanth Duddela,Daniel Krug,Hyun Uk Kim,Robert E. Bruccoleri,Sang Yup Lee,Sang Yup Lee,Michael A. Fischbach,Rolf Müller,Wolfgang Wohlleben,Rainer Breitling,Eriko Takano,Marnix H. Medema,Marnix H. Medema +14 more
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TLDR
AntiSMASH as mentioned in this paper is a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.org.Abstract:
Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.read more
Citations
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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Kai Blin,Simon Shaw,Katharina Steinke,Rasmus Villebro,Nadine Ziemert,Sang Yup Lee,Sang Yup Lee,Marnix H. Medema,Tilmann Weber +8 more
TL;DR: AntiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-Ri PPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines and provides more detailed predictions for type II polyketide synthase-encoding gene clusters.
Journal ArticleDOI
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Kai Blin,Thomas Wolf,Marc G. Chevrette,Xiaowen Lu,Christopher J. Schwalen,Satria A. Kautsar,Hernando G. Suarez Duran,Emmanuel L. C. de los Santos,Hyun Uk Kim,Mariana Nave,Jeroen S. Dickschat,Douglas A. Mitchell,Ekaterina Shelest,Rainer Breitling,Eriko Takano,Sang Yup Lee,Tilmann Weber,Marnix H. Medema +17 more
TL;DR: The thoroughly updated antiSMASH version 4 is presented, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, and several usability features have been updated and improved.
Journal ArticleDOI
antiSMASH 6.0: improving cluster detection and comparison capabilities.
Kai Blin,Simon Shaw,Alexander M. Kloosterman,Zach Charlop-Powers,Gilles P. van Wezel,Marnix H. Medema,Marnix H. Medema,Tilmann Weber +7 more
TL;DR: antiSMASH as mentioned in this paper is the most widely used tool for detecting and characterising biosynthetic gene clusters (BGCs) in bacteria and fungi, and it is updated version 6 of antiSMASH.
Journal ArticleDOI
Natural product discovery: past, present, and future
Leonard Katz,Richard H. Baltz +1 more
TL;DR: Advances in bioinformatics, mass spectrometry, proteomics, transcriptomics, metabolomics and gene expression are driving the new field of microbial genome mining for applications in natural product discovery and development.
Journal ArticleDOI
Minimum Information about a Biosynthetic Gene cluster.
Marnix H. Medema,Marnix H. Medema,Renzo Kottmann,Pelin Yilmaz,Matthew Cummings,John B. Biggins,Kai Blin,Irene de Bruijn,Yit-Heng Chooi,Yit-Heng Chooi,Jan Claesen,R. Cameron Coates,Pablo Cruz-Morales,Srikanth Duddela,Stephanie Düsterhus,Daniel J. Edwards,David P. Fewer,Neha Garg,Christoph Geiger,Juan Pablo Gomez-Escribano,Anja Greule,Michalis Hadjithomas,Anthony S. Haines,Eric J. N. Helfrich,Matthew L. Hillwig,Keishi Ishida,Adam C. Jones,Carla S. Jones,Katrin Jungmann,Carsten Kegler,Hyun Uk Kim,Hyun Uk Kim,Peter Kötter,Daniel Krug,Joleen Masschelein,Alexey V. Melnik,Simone M. Mantovani,Emily A. Monroe,Marcus A. Moore,Nathan A. Moss,Hans-Wilhelm Nützmann,Guohui Pan,Amrita Pati,Daniel Petras,F. Jerry Reen,Federico Rosconi,Zhe Rui,Zhenhua Tian,Nicholas J. Tobias,Yuta Tsunematsu,Yuta Tsunematsu,Philipp Wiemann,Elizabeth E. Wyckoff,Xiaohui Yan,Grace Yim,Fengan Yu,Yunchang Xie,Bertrand Aigle,Alexander Kristian Apel,Carl J. Balibar,Emily P. Balskus,Francisco Barona-Gómez,Andreas Bechthold,Helge B. Bode,Rainer Borriss,Sean F. Brady,Axel A. Brakhage,Patrick Caffrey,Yi-Qiang Cheng,Jon Clardy,Russell J. Cox,Russell J. Cox,René De Mot,Stefano Donadio,Mohamed S. Donia,Wilfred A. van der Donk,Wilfred A. van der Donk,Pieter C. Dorrestein,Sean Doyle,Arnold J. M. Driessen,Monika Ehling-Schulz,K. D. Entian,Michael A. Fischbach,Lena Gerwick,William H. Gerwick,Harald Gross,Bertolt Gust,Christian Hertweck,Christian Hertweck,Monica Höfte,Susan E. Jensen,Jianhua Ju,Leonard Katz,Leonard Kaysser,Jonathan L. Klassen,Nancy P. Keller,Jan Kormanec,Oscar P. Kuipers,Tomohisa Kuzuyama,Nikos C. Kyrpides,Nikos C. Kyrpides,Hyung Jin Kwon,Sylvie Lautru,Rob Lavigne,Chia Y. Lee,Bai Linquan,Xinyu Liu,Wen Liu,Andriy Luzhetskyy,Taifo Mahmud,Yvonne Mast,Carmen Méndez,Mikko Metsä-Ketelä,Jason Micklefield,Douglas A. Mitchell,Bradley S. Moore,Leonilde M. Moreira,Rolf Müller,Brett A. Neilan,Markus Nett,Jens Nielsen,Jens Nielsen,Fergal O'Gara,Fergal O'Gara,Hideaki Oikawa,Anne Osbourn,Marcia S. Osburne,Bohdan Ostash,Shelley M. Payne,Jean-Luc Pernodet,Miroslav Petricek,Jörn Piel,Olivier Ploux,Jos M. Raaijmakers,José A. Salas,Esther K. Schmitt,Barry Scott,Ryan F. Seipke,Ben Shen,David H. Sherman,Kaarina Sivonen,Michael J. Smanski,Margherita Sosio,Evi Stegmann,Roderich D. Süssmuth,Kapil Tahlan,Christopher M. Thomas,Yi Tang,Andrew W. Truman,Muriel Viaud,Jonathan D. Walton,Christopher T. Walsh,Tilmann Weber,Gilles P. van Wezel,Barrie Wilkinson,Joanne M. Willey,Wolfgang Wohlleben,Gerard D. Wright,Nadine Ziemert,Changsheng Zhang,Sergey B. Zotchev,Rainer Breitling,Eriko Takano,Frank Oliver Glöckner,Frank Oliver Glöckner +164 more
TL;DR: This work proposes the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard, to facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters.
References
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