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Genome Mining: History
Please note this is an old version of this entry, which may differ significantly from the current revision.
Contributor: Yu Peng

Genome mining is the systematic computational interrogation of genome sequence data to identify, annotate, and functionally infer genetically encoded biological features from characteristic sequence patterns and genomic organization. Within bioinformatics and molecular genomics, the process integrates sequence similarity searches, protein-domain recognition, motif analysis, gene-neighborhood information, comparative genomics, and specialized predictive algorithms to locate genes and coordinated genomic regions associated with defined molecular functions [1][2][3]. A major established form of genome mining identifies biosynthetic gene clusters, in which physically associated genes collectively encode enzymes, regulatory proteins, transport functions, and accessory components of a biosynthetic pathway [1][2]. Computational pipelines may classify these regions according to conserved biosynthetic domains, pathway architecture, similarity to characterized loci, and predicted enzymatic functions [1][3]. Genome mining therefore encompasses the extraction of biologically interpretable gene, pathway, and genomic-network information directly from assembled or annotated genome sequences through computational analysis and functional prediction [1][2][3].

  • Bioinformatics
  • genome annotation
  • biosynthetic gene clusters
  • comparative genomics

References

  1. Marnix H. Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A. Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling; AntiSMASH: Rapid Identification, Annotation and Analysis of Secondary Metabolite Biosynthesis Gene Clusters in Bacterial and Fungal Genome Sequences. Nucleic Acids Res. 2011, 39, W339-W346, 10.1093/nar/gkr466.
  2. Nadine Ziemert; Mohammad Alanjary; Tilmann Weber; The Evolution of Genome Mining in Microbes – A Review. Nat. Prod. Rep. 2016, 33, 988-1005, 10.1039/c6np00025h.
  3. Kai Blin; Simon Shaw; Hannah E Augustijn; Zachary L Reitz; Friederike Biermann; Mohammad Alanjary; Artem Fetter; Barbara R Terlouw; William W Metcalf; Eric J N Helfrich; et al. AntiSMASH 7.0: New and Improved Predictions for Detection, Regulation, Chemical Structures and Visualisation. Nucleic Acids Res. 2023, 51, W46-W50, 10.1093/nar/gkad344.
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