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Protocols

IMG-ABC specifications

Information


Unique identifier OMICS_09213
Name IMG-ABC
Alternative name Integrated Microbial Genomes-Atlas of Biosynthetic gene Clusters
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Publication for Integrated Microbial Genomes-Atlas of Biosynthetic gene Clusters

IMG-ABC citations

 (5)
library_books

Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS W 1 2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils

2018
Genes
PMCID: 5793183
PMID: 29324691
DOI: 10.3390/genes9010031

[…] ted sequences and SNPs assembled according to the Antibiotic Resistance Ontology (ARO). Biosynthetic gene clusters (BCs) represented within the genome of strain SRS-1-W-2016 were identified using the IMG-ABC (https://img.jgi.doe.gov/abc) pipeline, which is a repository of previously characterized BCs and associated secondary metabolites (SMs), respectively []. Protein families (pfams) within each […]

library_books

Draft genome sequence of Pseudomonas extremaustralis strain USBA GBX 515 isolated from Superparamo soil samples in Colombian Andes

2017
Stand Genomic Sci
PMCID: 5731063
PMID: 29255573
DOI: 10.1186/s40793-017-0292-9

[…] e same input but seeking C domains. The third and fourth runs were with FASTA amino acid files, seeking KS and C domains respectively. A list of all biosynthetic clusters is available through IMG and IMG-ABC systems [, ]. […]

call_split

SBSPKSv2: structure based sequence analysis of polyketide synthases and non ribosomal peptide synthetases

2017
Nucleic Acids Res
PMCID: 5570206
PMID: 28460065
DOI: 10.1093/nar/gkx344
call_split See protocol

[…] In the past decade, a large number of PKS and NRPS gene clusters have been identified and characterized. Resources like MIBig, IMG-ABC and antiSMASH database contain a large number of predicted secondary metabolite gene clusters (–). These databases are excellent resources containing a catalog of all predicted gene clusters a […]

library_books

In silico methods for linking genes and secondary metabolites: The way forward

2016
PMCID: 5640692
PMID: 29062931
DOI: 10.1016/j.synbio.2016.03.001

[…] identified gene clusters. Some of the major databases which have cataloged very large number of experimentally characterized PKS and NRPS clusters with known biosynthetic products are ClusterMine360, IMG-ABC and MIBiG. Apart from the sequence information and catalytic domain organization, major utility of these databases is to obtain the chemical structures of secondary metabolite products. Recent […]

library_books

IMG ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites

2015
MBio
PMCID: 4502231
PMID: 26173699
DOI: 10.1128/mBio.00932-15

[…] biosynthetic gene clusters. These analyses have been accessible only to laboratories staffed with computational biologists and with access to high-performance computing resources.For the first time, IMG-ABC links information regarding genomic pathways for the biosynthesis of secondary metabolites with chemical structure information on a scale of several thousand data sets. With careful efforts fo […]

Citations

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IMG-ABC institution(s)
Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Biosciences Computing, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
IMG-ABC funding source(s)
The Director, Office of Science, Office of Biological and Environmental Research, Life Sciences Division, U.S. Department of Energy (DE-AC02-05CH11231); National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy (DE-AC02-05CH11231).

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