Class 3 2009

1. Class 3 2009 European Resources Protein Focused

2. Protein Databases EBI – European Bioinformatics Institute http://www.ebi.ac.uk/

3. What is the difference between dealing with nucleotide DBs and protein DBs?

4. Name & description Gene encoded from Organism Function (only one?) Enzyme? Ligands? PTMs? Interactions? Biological processes. Structure. Sequence. Localization More... Protein information

5. Protein DB -short history Pre-UniProt Swiss-Prot: created in July 1986; since 1987, a collaboration of the SIB and the EMBL/EBI; TrEMBL: created at the EBI in 1996 as a computer-annotated protein sequence database supplementing Swiss-Prot. It was introduced to deal with the increased data flow from genome projects

6. PIR EBI SIB

7. The three-layered approach • The UniProt Archive (UniParc) • UniProtKB + all other protein sequences publicly available • Completeness • The UniProt Reference Clusters (UniRef) • Non-redundant views of UniProtKB + selected UniParcsets • Speed • The UniProt Knowledgebase (UniProtKB) • Central database of annotated protein sequences and functional information • UniProtKB/Swiss-Prot + UniProtKB/TrEMBL

8. Protein DBs • Swiss-Prot - manually annotated. • TrEMBL – translated EMBL, automatically annotated. • UniProtKB – The UniProt Knowledge • UniParc – The Achieve pf UniProt • PIR - Protein Information Resource • UniRef – The UniProt Reference Clusters • PDB – Protein Data Bank – structure • PRIDE – Resource for experimental proteomics (not in this class)

9. Databases growth www.genome.jp/en/db_growth.html

10. Protein DBs • Swiss-Prot - manually annotated 2005- ~100,000 2009 - ~400,000

11. . • TrEMBL – translated EMBL, automatically annotated.

13. Protein Names Different DBs – different accessions

14. Protein DBs • Swiss-Prot - manually annotated. • TrEMBL – translated EMBL, automatically annotated. • UniProtKB – The UniProt Knowledge • UniParc – The Achieve pf UniProt • PIR - Protein Information Resource • UniRef – The UniProt Reference Clusters • PDB – Protein Data Bank – structure • PRIDE – Resource for experimental proteomics (not in this class)

15. Principles

16. More in UniProt a complete annotated protein sequence database

17. Protein DBs • Swiss-Prot - manually annotated. • TrEMBL – translated EMBL, automatically annotated. • UniProtKB – The UniProt Knowledge • UniParc – The Achieve pf UniProt • PIR - Protein Information Resource • UniRef – The UniProt Reference Clusters • PDB – Protein Data Bank – structure • PRIDE – Resource for experimental proteomics (not in this class)

18. How is it built?

20. What’s in UniProt? http://beta.uniprot.org/

21. EBI interface

22. PIR – Protein Information Resource Integrated Protein Literature, Information and Knowledge Protein Family Classification System Integrated Protein Knowledgebase

23. ENDIf you got lost…(class exercise)some more slides…

24. EB-eye search

25. EB-eye search

27. NCBI - Entrez