The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more

被引：48
作者：
Blin, Kai [1 ]
Shaw, Simon [1 ]
Medema, Marnix H. [2 ]
Weber, Tilmann [1 ]
机构：
[1] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2800 Lyngby, Denmark
[2] Wageningen Univ, Bioinformat Grp, NL-6708 PB Wageningen, Netherlands
来源：
NUCLEIC ACIDS RESEARCH | 2023年 / 52卷 / D1期
基金：
新加坡国家研究基金会;
关键词：
TOOLS;
D O I：
10.1093/nar/gkad984
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Many microorganisms produce natural products that are frequently used in the development of medicines and crop protection agents. Genome mining has evolved into a prominent method to access this potential. antiSMASH is the most popular tool for this task. Here we present version 4 of the antiSMASH database, providing biosynthetic gene clusters detected by antiSMASH 7.1 in publicly available, dereplicated, high-quality microbial genomes via an interactive graphical user interface. In version 4, the database contains 231 534 high quality BGC regions from 592 archaeal, 35 726 bacterial and 236 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/. Graphical Abstract
引用
收藏
页码：D586 / D589
页数：4
相关论文
共 24 条
[1]   Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities [J].
Baltz, Richard H. .
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 2019, 46 (3-4) :281-299
[2]   antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation [J].
Blin, Kai ;
Shaw, Simon ;
Augustijn, Hannah E. ;
Reitz, Zachary L. ;
Biermann, Friederike ;
Alanjary, Mohammad ;
Fetter, Artem ;
Terlouw, Barbara R. ;
Metcalf, William W. ;
Helfrich, Eric J. N. ;
van Wezel, Gilles P. ;
Medema, Marnix H. ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2023, 51 (W1) :W46-W50
[3]   antiSMASH 6.0: improving cluster detection and comparison capabilities [J].
Blin, Kai ;
Shaw, Simon ;
Kloosterman, Alexander M. ;
Charlop-Powers, Zach ;
van Wezel, Gilles P. ;
Medema, Marnix H. ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2021, 49 (W1) :W29-W35
[4]   The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes [J].
Blin, Kai ;
Shaw, Simon ;
Kautsar, Satria A. ;
Medema, Marnix H. ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D639-D643
[5]   antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline [J].
Blin, Kai ;
Shaw, Simon ;
Steinke, Katharina ;
Villebro, Rasmus ;
Ziemert, Nadine ;
Lee, Sang Yup ;
Medema, Marnix H. ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2019, 47 (W1) :W81-W87
[6]   Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters [J].
Blin, Kai ;
Kim, Hyun Uk ;
Medema, Marnix H. ;
Weber, Tilmann .
BRIEFINGS IN BIOINFORMATICS, 2019, 20 (04) :1103-1113
[7]   The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters [J].
Blin, Kai ;
Andreu, Victoria Pascal ;
de los Santos, Emmanuel L. C. ;
Del Carratore, Francesco ;
Lee, Sang Yup ;
Medema, Marnix H. ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D625-D630
[8]   antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification [J].
Blin, Kai ;
Wolf, Thomas ;
Chevrette, Marc G. ;
Lu, Xiaowen ;
Schwalen, Christopher J. ;
Kautsar, Satria A. ;
Duran, Hernando G. Suarez ;
Santos, Emmanuel L. C. de los ;
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. .
NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W36-W41
[9]   The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters [J].
Blin, Kai ;
Medema, Marnix H. ;
Kottmann, Renzo ;
Lee, Sang Yup ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D555-D559
[10]   antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers [J].
Blin, Kai ;
Medema, Marnix H. ;
Kazempour, Daniyal ;
Fischbach, Michael A. ;
Breitling, Rainer ;
Takano, Eriko ;
Weber, Tilmann .
NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W204-W212
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