Integrated Microbial Genomes System

{{Short description|Genome browsing and annotation platform}}

{{infobox biodatabase

|title =IMG

|logo =Integrated microbial genomes.jpg

|logo_caption=Genome analysis tools in IMG 2.9

|description =Integrated microbial genomes database and comparative analysis system

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|author =Victor M Markowitz

|citation =Markowitz et al. (2012){{cite journal |last1=Markowitz|first1=Victor M|author2=Chen I-Min A |author3=Palaniappan Krishna |author4=Chu Ken |author5=Szeto Ernest |author6=Grechkin Yuri |author7=Ratner Anna |author8=Jacob Biju |author9=Huang Jinghua |author10=Williams Peter |author11=Huntemann Marcel |author12=Anderson Iain |author13=Mavromatis Konstantinos |author14=Ivanova Natalia N |author15=Kyrpides Nikos C|date=Jan 2012|title=IMG: the integrated microbial genomes database and comparative analysis system|journal=Nucleic Acids Research|volume=40|issue=1|pages=D115-22|location=England| pmid=22194640|doi=10.1093/nar/gkr1044| pmc=3245086}}

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|url ={{URL|http://img.jgi.doe.gov}}

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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.{{Cite journal |last1=Markowitz |first1=V. M. |last2=Chen |first2=I. M. A. |last3=Palaniappan |first3=K. |last4=Chu |first4=K. |last5=Szeto |first5=E. |last6=Grechkin |first6=Y. |last7=Ratner |first7=A. |last8=Anderson |first8=I. |last9=Lykidis |first9=A. |last10=Mavromatis |first10=K. |last11=Ivanova |first11=N. N. |last12=Kyrpides |first12=N. C. |title=The integrated microbial genomes system: An expanding comparative analysis resource |journal=Nucleic Acids Research |volume=38 |issue=Database issue |pages=D382–D390 |year=2009 |pmid=19864254 |pmc=2808961 |doi=10.1093/nar/gkp887}}{{Cite journal|last1=Hadjithomas|first1=Michalis|last2=Chen|first2=I.-Min Amy|last3=Chu|first3=Ken|last4=Ratner|first4=Anna|last5=Palaniappan|first5=Krishna|last6=Szeto|first6=Ernest|last7=Huang|first7=Jinghua|last8=Reddy|first8=T. B. K.|last9=Cimermančič|first9=Peter|date=2015-07-14|title=IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites|journal=mBio|volume=6|issue=4|pages=e00932|doi=10.1128/mBio.00932-15|issn=2150-7511|pmc=4502231|pmid=26173699}} 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.{{cn|date=April 2023}}

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.{{cite journal |first1=V. M. |first10=M. |first11=K. |first12=I. |first13=I. |first14=K. |first15=N. N. |first16=N. C. |last1=Markowitz |last11=Liolios |last12=Pagani |last13=Anderson |last14=Mavromatis |last15=Ivanova |last16=Kyrpides |last2=Chen |first2=I. -M. A. |last3=Chu |first3=K. |last4=Szeto |first4=E. |last5=Palaniappan |first5=K. |last6=Grechkin |first6=Y. |last7=Ratner |first7=A. |last8=Jacob |first8=B. |last9=Pati |first9=A. |last10=Huntemann |title=IMG/M: The integrated metagenome data management and comparative analysis system |journal=Nucleic Acids Research |year=2011 |volume=40 |issue=Database issue |pages=D123–D129 |doi=10.1093/nar/gkr975 |pmc=3245048 |pmid=22086953}}{{cite journal |title=IMG/M: integrated genome and metagenome comparative data analysis system |date=2017-01-04 |last1=Chen |first1=I.-Min A. |last2=Markowitz |first2=Victor M. |last3=Chu |first3=Ken |last4=Palaniappan |first4=Krishna |last5=Szeto |first5=Ernest |last6=Pillay |first6=Manoj |last7=Ratner |first7=Anna |last8=Huang |first8=Jinghua |last9=Andersen |first9=Evan |journal=Nucleic Acids Research |volume=45 |issue=D1 |pages=D507–D516 |issn=1362-4962 |doi=10.1093/nar/gkw929 |pmc=5210632 |pmid=27738135}} 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. 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.{{cite journal |title=IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project |date=2012 |bibcode=2012PLoSO...740151M |last1=Markowitz |first1=Victor M. |last2=Chen |first2=I.-Min A. |last3=Chu |first3=Ken |last4=Szeto |first4=Ernest |last5=Palaniappan |first5=Krishna |last6=Jacob |first6=Biju |last7=Ratner |first7=Anna |last8=Liolios |first8=Konstantinos |last9=Pagani |first9=Ioanna |journal=PLOS ONE |volume=7 |issue=7 |pages=e40151 |issn=1932-6203 |doi=10.1371/journal.pone.0040151 |pmc=3390314 |pmid=22792232| doi-access=free }} The IMG-ABC system is a system for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery.{{cite journal |title=IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes |date=2017-01-04 |last1=Hadjithomas |first1=Michalis |last2=Chen |first2=I.-Min A. |last3=Chu |first3=Ken |last4=Huang |first4=Jinghua |last5=Ratner |first5=Anna |last6=Palaniappan |first6=Krishna |last7=Andersen |first7=Evan |last8=Markowitz |first8=Victor |last9=Kyrpides |first9=Nikos C. |journal=Nucleic Acids Research |volume=45 |issue=D1 |pages=D560–D565 |issn=1362-4962 |doi=10.1093/nar/gkw1103 |pmc=5210574 |pmid=27903896}} 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.{{cite journal |title=IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses |date=2017-01-04 |last1=Paez-Espino |first1=David |last2=Chen |first2=I.-Min A. |last3=Palaniappan |first3=Krishna |last4=Ratner |first4=Anna |last5=Chu |first5=Ken |last6=Szeto |first6=Ernest |last7=Pillay |first7=Manoj |last8=Huang |first8=Jinghua |last9=Markowitz |first9=Victor M. |journal=Nucleic Acids Research |volume=45 |issue=D1 |pages=D457–D465 |issn=1362-4962 |doi=10.1093/nar/gkw1030 |pmc=5210529 |pmid=27799466}}{{cite journal |last1=Paez-Espino |first1=David |last2=Roux |first2=Simon |last3=Chen |first3=I-Min A |last4=Palaniappan |first4=Krishna |last5=Ratner |first5=Anna |last6=Chu |first6=Ken |last7=Huntemann |first7=Marcel |last8=Reddy |first8=T B K |last9=Pons |first9=Joan Carles |last10=Llabrés |first10=Mercè |last11=Eloe-Fadrosh |first11=Emiley A |last12=Ivanova |first12=Natalia N |last13=Kyrpides |first13=Nikos C |title=IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes |journal=Nucleic Acids Research |date=8 January 2019 |volume=47 |issue=D1 |pages=D678–D686 |doi=10.1093/nar/gky1127 |pmc=6323928 |pmid=30407573}}