Nikos Kyrpides Genome Biology Program GBP DOE Joint Genome institute IMG Genes Genomes Functions Metadata Clusters SNPs Proteomics Regulons Transcriptomes IMG Systems Data Types ID: 642214
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Slide1
The Integrated Microbial Genome (IMG) systems
Nikos
Kyrpides
Genome
Biology
Program (GBP)
DOE Joint Genome instituteSlide2
IMG
Genes
Genomes
Functions
Metadata
Clusters
SNPs
Proteomics
Regulons
Transcriptomes
IMG Systems Data TypesSlide3
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
Synteny
Gene Fusion
DotPlot
ACT
Co-
occurenceSlide4
Gene FusionsSlide5
Conserved chromosomal cassettes
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.
H
G
F
E
D
C
B
A
XI
X
IX
VII
VI
V
IV
III
II
I
Genes are replaced by protein families (
COGs
,
pfams
, IMG
ortholog
families).
One gene
multiple families.
Mavromatis
et al, (
2009)
PLoS
ONESlide6
Missing function from the
fatty acid biosynthesis pathway
No known gene for this function has
a homolog in
Streptococci
Missing Function context based
analysisSlide7
Genome
Synteny
toolsSlide8
IMG Function Curation
public & automatic
1. Protein Product
2. Protein FamilySlide9
IMG Function Curation(b) manual
4. MyIMG
3. IMG TermSlide10
IMG Function Curation
Automatic and Manual
1. Protein Product
3. IMG Term
4. MyIMG
2. Protein FamilySlide11
Who is there?Slide12
Finding organismsSlide13
What is the role of the organism in the community?Slide14
What is the metabolic potential of the community?
Function
AbundanceSlide15
Relative abundance of functions
Cloning bias.
PCR bias.
Assembly coverage.
Misassemblies
.
Erroneous gene prediction.Slide16
IMGcurationSlide17
Curation
checkSlide18Slide19
Gene annotation
curationSlide20
Gene pageSlide21Slide22