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

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

3. Protein information Name & description. Gene encoded from. Organism. Function. Enzyme? Ligands? PTMs? Interactions? Biological processes. Structure. Sequence. More...

4. Protein DBs Swiss-Prot - manually annotated. TrEMBL – translated EMBL, automatically annotated. RefSeq – Reference Sequence for proteins, currated. UniRef – The UniProt Reference Clusters. PIR - Protein Information Resource. PDB – Protein Data Bank – structure.

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

6. Protein Names Different DBs – different accessions AccessionsDB P12345TrEMBL MAPK_HUMANSwiss-Prot NP_123456 XP_123456 RefSeq UniRef100_P99999 UniRef90_P99999 UniRef50_P99999 UniRef ENSP00000123456Ensembl

7. EBI interface

8. EB-eye search

11. NCBI - Entrez

12. UniProt Knowledgebase UniProt Knowledgebase a complete annotated protein sequence database The Universal Protein Resource for protein sequences.UniProt A non-redundant archive of protein sequences extracted from public databases and contains only protein sequences. UniProt Archive Features clustering of similar sequences to yield a representative subset of sequences. This produces very fast search times. UniProt/UniRef A repository specifically developed for metagenomic and environmental data. UniProt/UniMES An annotated protein sequence database. Part of the UniProtKB. UniProtKB/Swiss- Prot A computer generated protein database enriched with automated classification and annotation. Part of the UniProtKB. UniProtKB/TrEMBL

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

14. How is it built?

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