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.
IMG
Genome analysis tools in IMG 2.9
Content
Description
Integrated microbial genomes database and comparative analysis system
In successive releases IMG has expanded to include several domain-specific tools. The Integrated Microbial Genomes with Microbiome Samples 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]
^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. PMC3390314. PMID 22792232.
^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. PMC5210574. PMID 27903896.
^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. PMC5210529. PMID 27799466.
^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. PMC6323928. PMID 30407573.
External links
Official website
MicrobesOnline
NCBI Microbial Genomes
TIGR Comprehensive Microbial Resource
The SEED
February 01, 2023
integrated, microbial, genomes, system, integrated, microbial, genomes, system, genome, browsing, annotation, platform, developed, department, energy, joint, genome, institute, contains, draft, complete, microbial, genomes, sequenced, integrated, with, other, . 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 IMGGenome analysis tools in IMG 2 9ContentDescriptionIntegrated microbial genomes database and comparative analysis systemContactAuthorsVictor M MarkowitzPrimary citationMarkowitz et al 2012 1 AccessWebsiteimg wbr jgi wbr doe wbr govIn 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 See also EditGenomes OnLine Database Genomics Metagenomics MicrobesOnlineReferences Edit 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 England 40 1 D115 22 doi 10 1093 nar gkr1044 PMC 3245086 PMID 22194640 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 Hadjithomas Michalis Chen I Min Amy Chu Ken Ratner Anna Palaniappan Krishna Szeto Ernest Huang Jinghua Reddy T B K Cimermancic 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 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 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 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 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 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 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 External links EditOfficial website IMG M home page MicrobesOnline NCBI Microbial Genomes TIGR Comprehensive Microbial Resource The SEED Retrieved from https en wikipedia org w index php title Integrated Microbial Genomes System amp oldid 1122534580, wikipedia, wiki, book, books, library,
