The Integrated Microbial Genome IMG systems Nikos Kyrpides

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

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

Gene/Genome context analysis tools Ø Gene Context Tools Gene Fusion • Gene Fusion Gene Synteny Cooccurence • Gene neighborhood • Gene co-occurrence Ø Genome Synteny Tools • VISTA (predetermined genome set) • Dot. Plot (two user specified genomes) • ACT (multiple user specified genomes) Dot. Plot ACT

Conserved chromosomal cassettes • Genes are replaced by protein families (COGs, pfams, IMG ortholog families). – One gene multiple families. I II IV V VI VII IX X XI A B C D E F G H • 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) PLo. S ONE

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

Genome Synteny tools

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

IMG Function Curation (b) manual 3. IMG Term 4. My. IMG

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

Who is there?

Finding organisms

What is the role of the organism in the community?

What is the metabolic potential of the community? Function Abundance

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

IMG curation

Curation check

Gene annotation curation

Gene page