A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

Standards in Genomic Sciences
Samuel C EpsteinMarnix H Medema

Abstract

Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.

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Citations

May 30, 2019·Current Genetics·Mikkel Rank NielsenJens Laurids Sørensen
Aug 29, 2020·Natural Product Reports·Jeffrey A van SantenRoger G Linington
Jan 6, 2019·Journal of Industrial Microbiology & Biotechnology·Nigel J MounceyYasuo Yoshikuni
Jan 8, 2020·Critical Reviews in Biotechnology·Huaxiang DengYujie Cai
Dec 29, 2020·Frontiers in Microbiology·Alinne L R Santana-PereiraMark R Liles
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Mar 25, 2021·Environmental Microbiome·Shiva Abdollahi Aghdam, Amanda May Vivian Brown
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Apr 28, 2021·Environmental Microbiome·Shiva Abdollahi Aghdam, Amanda May Vivian Brown
Mar 22, 2019·Journal of Natural Products·Jana BraeselAlessandra S Eustáquio

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Methods Mentioned

BETA
nuclear
X-ray

Software Mentioned

Google Scholar
Excel MIBiG
ChemDraw
althiomycin
antiSMASH
PubMed
GenBank
ChemSpider
chEMBL
of Science

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