Sequencing the World of Possibilities for Energy & Environment

IMG clusters – the hidden features

Sean Hooper

Genome Biology Program

JGI

Sequencing the World of Possibilities for Energy & Environment

Background

• Clusters work behind the scenes in IMG

• Used for– Data compression– Annotation assistance– Grouping of similar functions– Necessary for large datasets, e.g.

metagenomics

Sequencing the World of Possibilities for Energy & Environment

Example

• Search for a gene annotated as putative or hypothetical

• Study the often overlooked clusters of genes in IMG

Sequencing the World of Possibilities for Energy & Environment

Putative ribolase carboxylase

Sequencing the World of Possibilities for Energy & Environment

COG

Pfam

IMG

Sequencing the World of Possibilities for Energy & Environment

Tatusev et al 1997

1997: 720 cogs

2003: 4873 cogs

Sequencing the World of Possibilities for Energy & Environment

COG

Pfam

IMG

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

COG

Pfam

IMG

Sequencing the World of Possibilities for Energy & Environment

MCL clustering on sequence

Sequencing the World of Possibilities for Energy & Environment

Nodes = IMG genes

Edges = in same cluster

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Alignment detail

Sequencing the World of Possibilities for Energy & Environment

Phylogeny

• How do these clusters relate to phylogeny?

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Sequencing the World of Possibilities for Energy & Environment

Conclusions

• Provide fast access to related proteins

• Ease analysis and annotation (but cannot replace experimental work)

• Reveal substructures in function and phylogeny

Sequencing the World of Possibilities for Energy & Environment

Acknowledgements

Genome Biology

K Mavrommatis

IJ Anderson

NC Kyrpides

A Pati

IMG crew

K Palappian

E Szeto

VK Markowitz

Chalmers, Sweden

D Dalevi

Sequencing the World of Possibilities for Energy & Environment

COAL demo

• Cluster overview of Archaea

• Spectral bipartitioning

• Integrate metadata (phenotype, phylogeny)