title: IMG/M: integrated genome and metagenome comparative data analysis system.
abstract: The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA IMAChen@lbl.gov.
authors.forename: I-Min A
authors.initials: IA
authors.lastname: Chen
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Chu
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Ratner
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Huang
authors.affiliation: Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Andersen
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Varghese
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Michalis
authors.initials: M
authors.lastname: Hadjithomas
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Tennessen
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Torben
authors.initials: T
authors.lastname: Nielsen
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA nckyrpides@lbl.gov.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D019295:Computational Biology / Q000379:methods*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D012984:Software; D064878:Web Browser