Sequence databases: Difference between revisions
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[https://www.embl.de EMBL] | |||
[https://www.ncbi.nlm.nih.gov NCBI] | [https://www.ncbi.nlm.nih.gov NCBI] | ||
[https://img.jgi.doe.gov/ IMG/M] | |||
[https://genome.jgi.doe.gov/portal/ JGI Genome Portal] | |||
[https://antismash-db.secondarymetabolites.org/ AntiSMASH DB] <sup>1</sup> | |||
*A database with an overview of the available biosynthetic gene cluster predictions. It is possible to browse the database by phylogeny or secondary metabolite type. | |||
[https://mibig.secondarymetabolites.org/ MIBiG] <sup>2</sup> | |||
*Minimal information for Biosynthetic gene clusters. The Minimum Information about a Biosynthetic Gene cluster (MIBiG) contains annotations and metadata on experimentally validated biosynthetic gene clusters and their molecular products. | |||
[https://bigfam.bioinformatics.nl/home BIG FAM] <sup>3</sup> | |||
*BiG-FAM is a database of thousands of gene cluster families that captures the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). BiG-SLiCE is the algorithm behind BiG-FAM. | |||
#Kai Blin; Simon Shaw; Satria A. Kautsar; Marnix H. Medema; Tilmann Weber. (2020) The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes< em> Nucleic Acids Research </em>, gkaa978; doi: 10.1093/nar/gkaa978 | |||
#Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema, (2020) MIBiG 2.0: a repository for biosynthetic gene clusters of known function, <em>Nucleic Acids Research</em>, Volume 48, Issue D1, 08 January 2020, Pages D454–D458, https://doi.org/10.1093/nar/gkz882 | |||
#Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, (2021) <em> Nucleic Acids Research</em>, Volume 49, Issue D1, Pages D490–D497, https://doi.org/10.1093/nar/gkaa812 | |||
Latest revision as of 12:21, 18 November 2021
- A database with an overview of the available biosynthetic gene cluster predictions. It is possible to browse the database by phylogeny or secondary metabolite type.
MIBiG 2
- Minimal information for Biosynthetic gene clusters. The Minimum Information about a Biosynthetic Gene cluster (MIBiG) contains annotations and metadata on experimentally validated biosynthetic gene clusters and their molecular products.
BIG FAM 3
- BiG-FAM is a database of thousands of gene cluster families that captures the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). BiG-SLiCE is the algorithm behind BiG-FAM.
- Kai Blin; Simon Shaw; Satria A. Kautsar; Marnix H. Medema; Tilmann Weber. (2020) The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes< em> Nucleic Acids Research , gkaa978; doi: 10.1093/nar/gkaa978
- Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema, (2020) MIBiG 2.0: a repository for biosynthetic gene clusters of known function, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D454–D458, https://doi.org/10.1093/nar/gkz882
- Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, (2021) Nucleic Acids Research, Volume 49, Issue D1, Pages D490–D497, https://doi.org/10.1093/nar/gkaa812
