title: IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.
abstract: In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of "big" genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in Alphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules.
  
  
  OBJECTIVE
  IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.
authors.affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Michalis
authors.initials: M
authors.lastname: Hadjithomas
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: I-Min Amy
authors.initials: IM
authors.lastname: Chen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Chu
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Ratner
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Huang
authors.affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: T B K
authors.initials: TB
authors.lastname: Reddy
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Cimermančič
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Fischbach
authors.affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA apati@lbl.gov nckyrpides@lbl.gov.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA apati@lbl.gov nckyrpides@lbl.gov.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D051188:Knowledge Bases; D005810:Multigene Family; D064210:Secondary Metabolism / Q000235:genetics*