1. The Integrated Microbial Genome (IMG) systems
Nikos Kyrpides
Genome Biology Program (GBP)
DOE Joint Genome institute 1

2. IMG IMG Systems Data Types Genes SNPs Proteomics Regulons Genomes
Functions
Metadata
Clusters
IMG
SNPs
Proteomics
Regulons
Transcriptomes

3. Gene/Genome context analysis tools
Gene Context Tools
Gene Fusion
Gene neighborhood
Gene co-occurrence
Genome Synteny Tools
VISTA (predetermined genome set)
DotPlot (two user specified genomes)
ACT (multiple user specified genomes)
Gene Fusion
Gene Synteny
Co-occurence
DotPlot
ACT

4. Gene Fusions

5. Conserved chromosomal cassettes
Genes are replaced by protein families (COGs, pfams, IMG ortholog families).
One gene  multiple families. H G F E D C B A XI X IX
VII VI V IV
III II I
Conserved chromosomal cassette contains:
cassettes that share at least TWO protein families,
protein families that cassettes have in common.
The definition of conserved chromosomal cassette does not take into account the order of the protein families on the cassette.
Mavromatis et al, (2009) PLoS ONE

6. Missing Function context based analysis
Missing function from the fatty acid biosynthesis pathway
No known gene for this function has
a homolog in Streptococci

7. Genome Synteny tools

8. IMG Function Curation 1. Protein Product 2. Protein Family
public & automatic
1. Protein Product
2. Protein Family

9. IMG Function Curation
(b) manual
3. IMG Term
4. MyIMG

10. IMG Function Curation 1. Protein Product 2. Protein Family 3. IMG Term
Automatic and Manual
1. Protein Product
2. Protein Family
3. IMG Term
4. MyIMG

11. Who is there?

12. Finding organisms

13. What is the role of the organism in the community?

14. What is the metabolic potential of the community?
Function
Abundance

15. Relative abundance of functions
Cloning bias.
PCR bias.
Assembly coverage.
Misassemblies.
Erroneous gene prediction.

16. IMG
curation

17. Curation check

19. Gene annotation curation
Allows overview comparisons between cluster (family) and gene annotations to identify over and underclassified genes

20. Gene page
Main gene detail page