Integrated Microbial Genomes System

IMG
Genome analysis tools in IMG 2.9
Content
DescriptionIntegrated microbial genomes database and comparative analysis system
Contact
AuthorsVictor M Markowitz
Primary citationMarkowitz et al. (2012)[1]
Access
Websiteimg.jgi.doe.gov

The Integrated Microbial Genomes (IMG) system is a genome browsing and annotation platform developed by the U.S. Department of Energy (DOE)-Joint Genome Institute.[2][3] IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes (including Archaea, Bacteria, Eukarya, Viruses and Plasmids). IMG provides users a set of tools for comparative analysis of microbial genomes along three dimensions: genes, genomes and functions. Users can select and transfer them in the comparative analysis carts based upon a variety of criteria. IMG also includes a genome annotation pipeline that integrates information from several tools, including KEGG, Pfam, InterPro, and the Gene Ontology, among others. Users can also type or upload their own gene annotations (called MyIMG gene annotations) and the IMG system will allow them to generate Genbank or EMBL format files containing these annotations.[citation needed]

In successive releases IMG has expanded to include several domain-specific tools. The Integrated Microbial Genomes with Microbiome Samples (IMG/M) system is an extension of the IMG system providing a comparative analysis context of assembled metagenomic data with the publicly available isolate genomes.[4][5] The Integrated Microbial Genomes- Expert Review (IMG/ER) system provides support to individual scientists or group of scientists for functional annotation and curation of their microbial genomes of interest.[2] Users can submit their annotated genomes (or request the IMG automated annotation pipeline to be applied first) into IMG-ER and proceed with manual curation and comparative analysis in the system, through secure (password protected) access. The IMG-HMP is focused on analysis of genomes related to the Human Microbiome Project (HMP) in the context of all publicly available genomes in IMG.[6] The IMG-ABC system is a system for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery.[7] The IMG-VR system (with the recent updated version IMG/VR v.2.0) is the largest publicly available database for viral genomes and metagenomes.[8][9]

  1. ^ Markowitz, Victor M; Chen I-Min A; Palaniappan Krishna; Chu Ken; Szeto Ernest; Grechkin Yuri; Ratner Anna; Jacob Biju; Huang Jinghua; Williams Peter; Huntemann Marcel; Anderson Iain; Mavromatis Konstantinos; Ivanova Natalia N; Kyrpides Nikos C (Jan 2012). "IMG: the integrated microbial genomes database and comparative analysis system". Nucleic Acids Res. 40 (1). England: D115-22. doi:10.1093/nar/gkr1044. PMC 3245086. PMID 22194640.
  2. ^ a b Markowitz, V. M.; Chen, I. M. A.; Palaniappan, K.; Chu, K.; Szeto, E.; Grechkin, Y.; Ratner, A.; Anderson, I.; Lykidis, A.; Mavromatis, K.; Ivanova, N. N.; Kyrpides, N. C. (2009). "The integrated microbial genomes system: An expanding comparative analysis resource". Nucleic Acids Research. 38 (Database issue): D382–D390. doi:10.1093/nar/gkp887. PMC 2808961. PMID 19864254.
  3. ^ Hadjithomas, Michalis; Chen, I.-Min Amy; Chu, Ken; Ratner, Anna; Palaniappan, Krishna; Szeto, Ernest; Huang, Jinghua; Reddy, T. B. K.; Cimermančič, Peter (2015-07-14). "IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites". mBio. 6 (4): e00932. doi:10.1128/mBio.00932-15. ISSN 2150-7511. PMC 4502231. PMID 26173699.
  4. ^ Markowitz, V. M.; Chen, I. -M. A.; Chu, K.; Szeto, E.; Palaniappan, K.; Grechkin, Y.; Ratner, A.; Jacob, B.; Pati, A.; Huntemann, M.; Liolios, K.; Pagani, I.; Anderson, I.; Mavromatis, K.; Ivanova, N. N.; Kyrpides, N. C. (2011). "IMG/M: The integrated metagenome data management and comparative analysis system". Nucleic Acids Research. 40 (Database issue): D123–D129. doi:10.1093/nar/gkr975. PMC 3245048. PMID 22086953.
  5. ^ Chen, I.-Min A.; Markowitz, Victor M.; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan (2017-01-04). "IMG/M: integrated genome and metagenome comparative data analysis system". Nucleic Acids Research. 45 (D1): D507–D516. doi:10.1093/nar/gkw929. ISSN 1362-4962. PMC 5210632. PMID 27738135.
  6. ^ Markowitz, Victor M.; Chen, I.-Min A.; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna (2012). "IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project". PLOS ONE. 7 (7): e40151. Bibcode:2012PLoSO...740151M. doi:10.1371/journal.pone.0040151. ISSN 1932-6203. PMC 3390314. PMID 22792232.
  7. ^ Hadjithomas, Michalis; Chen, I.-Min A.; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Markowitz, Victor; Kyrpides, Nikos C. (2017-01-04). "IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes". Nucleic Acids Research. 45 (D1): D560–D565. doi:10.1093/nar/gkw1103. ISSN 1362-4962. PMC 5210574. PMID 27903896.
  8. ^ Paez-Espino, David; Chen, I.-Min A.; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M. (2017-01-04). "IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses". Nucleic Acids Research. 45 (D1): D457–D465. doi:10.1093/nar/gkw1030. ISSN 1362-4962. PMC 5210529. PMID 27799466.
  9. ^ Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. (2019). "IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes". Nucleic Acids Res. 47 (D1): D678–D686. doi:10.1093/nar/gky1127. PMC 6323928. PMID 30407573.