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:

Hadjithomas, Michalis ^[1]; Chen, I-Min A. ^[2]; Chu, Ken ^[2]; Huang, Jinghua ^[2]; Ratner, Anna ^[2]; Palaniappan, Krishna ^[2]; Andersen, Evan ^[2]; Markowitz, Victor ^[2]; Kyrpides, Nikos C. ^[1]; Ivanova, Natalia N. ^[1]

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+ Show Author Affiliations

1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biosciences Computing

Publication Date:

Tue Nov 29 00:00:00 EST 2016

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1379643

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

Nucleic Acids Research

Additional Journal Information:

Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048

Publisher:

Oxford University Press

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; metabolism; cancer; foreign medical graduates; genes; genome; graphical displays; gene cluster; biopharmaceutics classification system; metabolites; verification