Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters
作者： Natalie D. Fedorova , Venkatesh Moktali , Marnix H. Medema
DOI: 10.1007/978-1-62703-122-6_2
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摘要: The accelerating pace of microbial genomics is sparking a renaissance in the field natural products research. Researchers can now get preview organism's secondary metabolome by analyzing its genomic sequence. Combined with other -omics data, this approach may provide cost-effective alternative to industrial high-throughput screening drug discovery. In last few years, several computational tools have been developed facilitate process identifying genes involved metabolite biosynthesis bacterial and fungal genomes. Here, we review seven software programs that are available for purpose, an emphasis on antibiotics & Secondary Metabolite Analysis SHell (antiSMASH) Unknown Regions Finder (SMURF), only comprehensively detect complete gene clusters. We also discuss five related packages-CLUster SEquence ANalyzer (CLUSEAN), ClustScan, Structure Based Sequence Polyketide Synthases (SBSPKS), NRPSPredictor, Natural Product searcher (NP.searcher)-that identify backbone genes. This chapter offers detailed protocols, suggestions, caveats assist researchers using these most effectively.
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