AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, 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, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
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Language: | English |
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dig-wur-nl-wurpubs-5243912024-10-01 Blin, Kai Wolf, Thomas Chevrette, Marc G. Lu, Xiaowen Schwalen, Christopher J. Kautsar, Satria A. Suarez Duran, Hernando G. De Los Santos, Emmanuel L.C. Kim, Hyun Uk Nave, Mariana Dickschat, Jeroen S. Mitchell, Douglas A. Shelest, Ekaterina Breitling, Rainer Takano, Eriko Lee, Sang Yup Weber, Tilmann Medema, Marnix H. Article/Letter to editor Nucleic acids research 45 (2017) W1 ISSN: 0305-1048 AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification 2017 Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, 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, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules. en application/pdf https://research.wur.nl/en/publications/antismash-40-improvements-in-chemistry-prediction-and-gene-cluste 10.1093/nar/gkx319 https://edepot.wur.nl/420215 Life Science https://creativecommons.org/licenses/by/4.0/ Wageningen University & Research |
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Life Science Life Science Blin, Kai Wolf, Thomas Chevrette, Marc G. Lu, Xiaowen Schwalen, Christopher J. Kautsar, Satria A. Suarez Duran, Hernando G. De Los Santos, Emmanuel L.C. Kim, Hyun Uk Nave, Mariana Dickschat, Jeroen S. Mitchell, Douglas A. Shelest, Ekaterina Breitling, Rainer Takano, Eriko Lee, Sang Yup Weber, Tilmann Medema, Marnix H. AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
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Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, 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, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules. |
format |
Article/Letter to editor |
topic_facet |
Life Science |
author |
Blin, Kai Wolf, Thomas Chevrette, Marc G. Lu, Xiaowen Schwalen, Christopher J. Kautsar, Satria A. Suarez Duran, Hernando G. De Los Santos, Emmanuel L.C. Kim, Hyun Uk Nave, Mariana Dickschat, Jeroen S. Mitchell, Douglas A. Shelest, Ekaterina Breitling, Rainer Takano, Eriko Lee, Sang Yup Weber, Tilmann Medema, Marnix H. |
author_facet |
Blin, Kai Wolf, Thomas Chevrette, Marc G. Lu, Xiaowen Schwalen, Christopher J. Kautsar, Satria A. Suarez Duran, Hernando G. De Los Santos, Emmanuel L.C. Kim, Hyun Uk Nave, Mariana Dickschat, Jeroen S. Mitchell, Douglas A. Shelest, Ekaterina Breitling, Rainer Takano, Eriko Lee, Sang Yup Weber, Tilmann Medema, Marnix H. |
author_sort |
Blin, Kai |
title |
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
title_short |
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
title_full |
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
title_fullStr |
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
title_full_unstemmed |
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
title_sort |
antismash 4.0 - improvements in chemistry prediction and gene cluster boundary identification |
url |
https://research.wur.nl/en/publications/antismash-40-improvements-in-chemistry-prediction-and-gene-cluste |
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