Comprehensive Coverage and Annotation of Proteome Space

The UniProt Knowledgebase (UniProtKB) endeavours to provide the scientific community with the most comprehensive catalogue possible of protein sequence and functional information. To achieve this, we have put in place procedures that gather data accurately and consistently from source databases followed by extensive annotation and cross-referencing to other resources. The increasing efficiency of whole genome sequencing has led to an unprecedented rise in the release rate of fully sequenced genomes. At UniProt, we provide comprehensive protein-centric views of such genomes through the Proteomes portal (http://www.uniprot.org/proteomes/).

Complete proteomes are based on translations of completely sequenced genomes; in addition, we offer a selected subset of reference proteomes including those of rice, wheat, maize, cow, pig, sheep and other commercially important species. These reference proteomes are the focus of expert curation thus providing a basis for the automatic annotation less well-studied genomes. Experimental data from the literature, genome scale data such as gene expression and proteomics studies, protein-protein interactions and pathway data are all used in the annotation of these protein sets.

In addition to the import of new proteomes, maintenance and updating of existing proteomes to reflect improvements in genome assemblies and genebuild procedures is a vital part the proteomes project. We receive regular updates and feedback from annotation efforts thus benefiting the larger research community.

The talk will outline the production process for complete and reference proteomes, different ways of accessing this data and recent developments in the annotation of proteomes.