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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

Class 3 2009

European Resources

Protein Focused


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

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


Protein information

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
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
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
Databases growth

www.genome.jp/en/db_growth.html


Protein dbs1
Protein DBs

  • Swiss-Prot - manually annotated

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


.

  • TrEMBL – translated EMBL, automatically annotated.


Protein names
Protein Names

Different DBs – different accessions


Protein dbs2
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)



More in uniprot a complete annotated protein sequence database
More in UniProt a complete annotated protein sequence database


Protein dbs3
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)



What’s in UniProt?

http://beta.uniprot.org/



Pir protein information resource
PIR – Protein Information Resource

Integrated Protein Literature, Information and Knowledge

Protein Family Classification System

Integrated Protein Knowledgebase


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





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