Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System
Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.
Key WordsComparative genome data analysis integrated microbial genomes occurrence profiles microbial genome data management comparative genome data analysis gene occurrence profile functional occurrence profile gene model validation integrated microbial genomes
We thank Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Iain Anderson, Natalia Ivanova, Athanasios Lykidis, Kostas Mavrommatis, Phil Hugenholtz, Anu Padki, Kristen Taylor, Xueling Zhao, Shane Brubaker, Greg Werner, and Inna Dubchak for their contribution to the development and maintenance of IMG. With their comments and suggestions, Krishna Palaniappan and Iain Anderson helped improve the examples in this chapter. Eddy Rubin and James Bristow provided, support, advice, and encouragement throughout the IMG project. IMG uses tools and data from a number of publicly available resources, their availability and value is gratefully acknowledged. The work presented in this paper was supported by the Director, Office of Science, Office of Biological and Environmental Research, Life Sciences Division, US Department of Energy under contract no. DE-AC03-76SF00098.
- 7.Gene Ontology Consortium. (2004) The Gene Ontology Database and Informatics Resource. Nucleic Acids Res. 32, 258–261.Google Scholar
- 11.Hauser, L., Larimer, F., Land, M., Shah, M., and Uberbacher, E. (2004) Analysis and annotation of microbial genome sequences. Genet. Eng. 26, 225–238.Google Scholar
- 13.BioPAX. (2006) Biological Pathways Exchange. http://www.biopax.org/.
- 15.Osterman, A. and Overbeek, R. (2003) Missing genes in metabolic pathways: a comparative genomic approach. Chem. Biol. 7, 238–251.Google Scholar