The integrated microbial genomes (IMG) system

By Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anuradha Padki, Xu Zhao, I-Min A. Dubchak, Philip Hugenholtz, Iain Anderson and 4 more. Nucleic Acids Res., 2005

437 citations recorded by the source corpus.

The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for analyzing genomes, genes and functions, individually or in a comparative context. IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at .

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f962cbba7c0e89e936cf028345c26288ad86e036

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Nikos Kyrpides
2. Steven L. Salzberg
3. I-Min A. Chen
4. Natalia N. Ivanova
5. Victor Kunin
6. Krishna Palaniappan
7. Victor M. Markowitz
8. Alla L. Lapidus

In Plant Science

1. Natalia N. Ivanova
2. I-Min A. Chen
3. Zaida Luthey-Schulten
4. Robert A. Edwards
5. Philip Hugenholtz
6. Marcel Huntemann
7. Nikos Kyrpides
8. John Eargle

Citations in the corpus

• Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils (2009, neutral): “Integrated Microbial Genomes system (55) (http://img.”
• A Bioinformatician's Guide to Metagenomics (2008, background): “A parallelized implementation of BLAST, ScalaBLAST (101), is used to precompute all pairwise gene similarities at the amino acid level for IMG/M, reducing the computation time by 30-fold (90).”
• The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata (2007, background): “These include (a) GreenGenes IDs (19); (b) StrainInfo IDs (20); (c) GCAT IDs (21) and (d) IMG IDs (22).”
• Use of simulated data sets to evaluate the fidelity of metagenomic processing methods (2007, methodology): “Selected data sets are also available in the IMG/M 24 system, which facilitates their analysis and the identification of errors.”
• IMG/M: a data management and analysis system for metagenomes (2007, methodology): “IMG/M consists of microbial metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system (11).”
• IMG: the integrated microbial genomes database and comparative analysis system (2011, methodology): “We review below IMG’s data content growth and analysis tool extensions since the last published report on IMG (23).”
• MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, background): “The total size of the sequence databases (NCBI [7,8], EMBL [9], DDBJ [10], JGI [11], RDP [12], Swiss-Prot/TrEMBL [13], CRW [14], Bayreuth tRNA compila-tions [15], and the Genomic tRNA Database [16]) is several orders of magnitude greater than that of the structure databases.”
• Ecology drives a global network of gene exchange connecting the human microbiome (2011, background): “to calculate an all-against-all nucleotide alignment for 2,235 genomes downloaded from IM”
• RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes (2015, methodology): “RAST and other annotation engines encapsulate software for identifying and annotating specific genomic features into a standard annotation pipeline 11–16 .”
• IMG ER: a system for microbial genome annotation expert review and curation (2009, neutral): “Contact: vmmarkowitz@lbl.gov Supplementary information: Supplementary data are available at Bioinformatics online.”
• Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees (2008, background): “tem (22) and with the basic local alignment search tool (BLAST) (1).”
• The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools (2012, neutral): “Widely used metagenome analysis systems like IMG/M[4] and MG-RAST[5] employ substantial computational resources while computing sequence similarity results.”