Protein Databases

Protein Databases

EBI – European Bioinformatics Institute

http://www.ebi.ac.uk/

What is the difference between

dealing with nucleotide DBs and

protein DBs?

Protein information

Name & description.

Gene encoded from.

Organism.

Function.

Enzyme? Ligands?

PTMs? Interactions?

Biological processes.

Structure.

Sequence.

More...

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.

Databases growth

www.genome.jp/en/db_growth.html

Protein NamesDifferent DBs – different accessions

DBAccessions

TrEMBLP12345

Swiss-ProtMAPK_HUMAN

RefSeqNP_123456

XP_123456

UniRefUniRef100_P99999

UniRef90_P99999

UniRef50_P99999

EnsemblENSP00000123456

EBI interface

EB-eye search

EB-eye search

NCBI - Entrez

UniProt Knowledgebase a complete annotated protein sequence database

UniProtThe Universal Protein Resource for protein sequences .

UniProt ArchiveA non-redundant archive of protein sequences extracted from public databases and contains only protein sequences.

UniProt/UniRefFeatures clustering of similar sequences to yield a representative subset of sequences. This produces very fast search times.

UniProt/UniMESA repository specifically developed for metagenomic and environmental data.

UniProtKB/Swiss-Prot

An annotated protein sequence database. Part of the UniProtKB.

UniProtKB/TrEMBLA computer generated protein database enriched with automated classification and annotation. Part of the UniProtKB.

http://beta.uniprot.org/

What’s in UniProt?

How is it built?

PIR – Protein Information Resource

Protein Family Classification System

Integrated

Protein

Knowledgebase

Integrated Protein Literature, Information and Knowledge