Class 3 2009
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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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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?)

Enzyme?

Ligands?

PTMs?

Interactions?

Biological processes.

Structure.

Sequence.

Localization

More...

Protein information


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


PIR

EBI

SIB


  • 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


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)


Databases growth

www.genome.jp/en/db_growth.html


Protein DBs

  • Swiss-Prot - manually annotated

    2005- ~100,000 2009 - ~400,000


.

  • TrEMBL – translated EMBL, automatically annotated.


Protein Names

Different DBs – different accessions


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)


Principles


More in UniProt a complete annotated protein sequence database


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)


How is it built?


What’s in UniProt?

http://beta.uniprot.org/


EBI interface


PIR – Protein Information Resource

Integrated Protein Literature, Information and Knowledge

Protein Family Classification System

Integrated Protein Knowledgebase


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


EB-eye search


EB-eye search


NCBI - Entrez


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