Genome Designs' Public Projects

In the beginning of the genomics era, sequenced genomes raised the interest of the entire community, and every interested party contributed to the annotation. Now the newly sequenced and automatically annotated genomes appear in spades and stay untouched and often unnoticed by the community and public services, and even their authors often lack funding for the improvement of their annotation.

The automatic annotations are often incomplete, and their missing or erroneous gene assignments get propagated throughout the new annotations. Genome Designs strives to improve the quality of genome annotations by manually annotating sample public genomes and augmenting the pool of public knowledge.

Below we present comparative statistics for several re-annotated and reconstructed archaeal genomes. These archaeal organisms were selected for their well known difficulty for annotation, because in their small genomes, proteins tend to be multi-functional. A major break-through in this work was achieved by parallel genome annotation and metabolic reconstruction. The new annotation and reconstructions for Desulfurococcus Kamchatkensis are available for download.

Desulfurococcus Kamchatkensis Data from UniProt Genome Designs'
ORFs 1470 1470
Uncharacterized Protein ORFs 443 45*
Uncharacterized Proteins (%) 30.1 3.0*
Annotated ORFs with EC 90 964
% Annotated ORFs with EC 6.1 65.6

*Partially characterized proteins, at least up to cellular localization

Downloads for Desulfurococcus Kamchatkensis

Complete re-annotation (.xls)
Intermediary Metabolism Outline*
Carbohydrate Intermediate Metabolism*
Purine Metabolism*
Pyrimidine Metabolism*
Aspartate and Glutamate Metabolism*
Branched Chain Amino Acid Biosynthesis*

*Hyperlinked diagram, best viewed in Microsoft IE