title: IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.
abstract: Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA michalis@lbl.gov.
authors.forename: Michalis
authors.initials: M
authors.lastname: Hadjithomas
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: I-Min A
authors.initials: IA
authors.lastname: Chen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Chu
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Huang
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Ratner
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Andersen
authors.affiliation: Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA nnivanova@lbl.gov.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D012984:Software; D064878:Web Browser