Class 3 2009
This presentation is the property of its rightful owner.
Sponsored Links
1 / 27

Class 3 2009 PowerPoint PPT Presentation


  • 41 Views
  • Uploaded on
  • Presentation posted in: General

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?)

Download Presentation

Class 3 2009

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


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


Class 3 2009

PIR

EBI

SIB


Class 3 2009

  • 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


Class 3 2009

.

  • 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)


Principles

Principles


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)


How is it built

How is it built?


Class 3 2009

What’s in UniProt?

http://beta.uniprot.org/


Ebi interface

EBI interface


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…


Eb eye search

EB-eye search


Eb eye search1

EB-eye search


Ncbi entrez

NCBI - Entrez


  • Login