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Protein Databases EBI – European Bioinformatics Institute

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Presentation on theme: "Protein Databases EBI – European Bioinformatics Institute"— Presentation transcript:

1 Protein Databases EBI – European Bioinformatics Institute

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

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 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

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