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IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

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 cluster...

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Autores principales: Hadjithomas, Michalis, Chen, I-Min A., Chu, Ken, Huang, Jinghua, Ratner, Anna, Palaniappan, Krishna, Andersen, Evan, Markowitz, Victor, Kyrpides, Nikos C., Ivanova, Natalia N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210574/
https://www.ncbi.nlm.nih.gov/pubmed/27903896
http://dx.doi.org/10.1093/nar/gkw1103
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author Hadjithomas, Michalis
Chen, I-Min A.
Chu, Ken
Huang, Jinghua
Ratner, Anna
Palaniappan, Krishna
Andersen, Evan
Markowitz, Victor
Kyrpides, Nikos C.
Ivanova, Natalia N.
author_facet Hadjithomas, Michalis
Chen, I-Min A.
Chu, Ken
Huang, Jinghua
Ratner, Anna
Palaniappan, Krishna
Andersen, Evan
Markowitz, Victor
Kyrpides, Nikos C.
Ivanova, Natalia N.
author_sort Hadjithomas, Michalis
collection PubMed
description 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.
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spelling pubmed-52105742017-01-05 IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes Hadjithomas, Michalis Chen, I-Min A. Chu, Ken Huang, Jinghua Ratner, Anna Palaniappan, Krishna Andersen, Evan Markowitz, Victor Kyrpides, Nikos C. Ivanova, Natalia N. Nucleic Acids Res Database Issue 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. Oxford University Press 2017-01-04 2016-11-28 /pmc/articles/PMC5210574/ /pubmed/27903896 http://dx.doi.org/10.1093/nar/gkw1103 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Hadjithomas, Michalis
Chen, I-Min A.
Chu, Ken
Huang, Jinghua
Ratner, Anna
Palaniappan, Krishna
Andersen, Evan
Markowitz, Victor
Kyrpides, Nikos C.
Ivanova, Natalia N.
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title_full IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title_fullStr IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title_full_unstemmed IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title_short IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
title_sort img-abc: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210574/
https://www.ncbi.nlm.nih.gov/pubmed/27903896
http://dx.doi.org/10.1093/nar/gkw1103
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