IMG: Integrated Microbial Genomes
IMG: Integrated Microbial Genomes

AboutIMG/EDU

The Integrated Microbial Genomes- Education Site (IMG/EDU) system provides training and teaching support for genome analysis applied to the annotation of microbial genomes in the comparative context of all the genomes available in IMG. IMG/EDU is developed jointly by the Genome Biology Program at DOE's Joint Genome Institute and the Biological Data Management and Technology Center (BDMTC) at Lawrence Berkeley National Laboratory, with suggestions provided by the IMG/EDU Advisory Board.

IMG/EDU provides all the analytical tools available in IMG, but its main purpose is to support the curation of product names and a number of associated annotations, using IMG's MyIMG tools (see IMG/EDU Tutorial). IMG/EDU users will be able to focus on a genome that is already available in IMG/EDU or submit a new genome for inclusion into IMG/EDU, whereby this genome has predicted genes and associated functional annotations. Annotations can be restricted to specific training groups/classes or made publicly available.

IMG/EDU genome baseline consists of all isolate genomes in IMG. All baseline genomes are collected from RefSeq and reflect the annotations of the sequencing centers that have submitted them. For bacterial and archaeal genomes sequenced at JGI, the default gene model and product name assignments are generated using the automatic Genome Analysis Pipeline at Oak Ridge National Lab (ORNL) [1].

Gene models and product names assignments for a genome that is not part of the IMG genome baseline can be generated outside IMG as follows:

  1. Gene models are mandatory for bacterial and archaeal genomes and can be generated by employing one of several methods, including:
    1. GeneMark by submitting genomes to NCBI's Microbial Genome Annotation site at: http://www.ncbi.nlm.nih.gov/genomes/MICROBES/genemark.cgi
    2. Glimmer by submitting genomes to NCBI's Microbial Genome Annotation site at: http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi.

  2. Product names are not mandatory. Thus, all genes can be assigned "hypothetical protein" names. Alternatively, product names can be assigned to genes by:
    1. using a specific annotation pipeline prior to inclusion into IMG EDU; or
    2. applying IMG's product name assignment method that is applied to genomes after they are loaded into IMG.

All finished JGI genomes undergo expert review and manual curation of gene models that were generated using the ORNL pipeline [1]. The gene models of all public archaeal genomes have been also manually curated before inclusion into IMG, with both original and curated gene models available at: IMG/QA. For details on JGI's gene model curation, see: http://img.jgi.doe.gov/archaeal_qa/doc/news_index.html.

References

  1. Hauser, L., Larimer, F., Land, M., Shah, M., and Uberbacher, E. (2004) Analysis and Annotation of Microbial Genome Sequences, Genetic Engineering, 26, Kluwer Academic/Plenum Publishers, 225-238.