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Class 3 2009

Class 3 2009. European Resources Protein Focused. Protein Databases. EBI – European Bioinformatics Institute http://www.ebi.ac.uk/. What is the difference between dealing with nucleotide DBs and protein DBs?. Name & description Gene encoded from Organism Function (only one?)

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Class 3 2009

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  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.

  12. Protein Names Different DBs – different accessions

  13. 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)

  14. Principles

  15. More in UniProt a complete annotated protein sequence database

  16. 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)

  17. How is it built?

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

  19. EBI interface

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

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

  22. EB-eye search

  23. EB-eye search

  24. NCBI - Entrez

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