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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?. Name & description. Gene encoded from. Organism. Function . Enzyme? Ligands? PTMs? Interactions?. Biological processes.

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Protein Databases

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  1. Protein Databases EBI – European Bioinformatics Institute http://www.ebi.ac.uk/

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

  3. Name & description. Gene encoded from. Organism. Function. Enzyme? Ligands? PTMs? Interactions? Biological processes. Structure. Sequence. More... Protein information

  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 www.genome.jp/en/db_growth.html

  6. Protein Names Different DBs – different accessions

  7. EBI interface

  8. EB-eye search

  9. EB-eye search

  10. NCBI - Entrez

  11. UniProt Knowledgebasea complete annotated protein sequence database

  12. What’s in UniProt? http://beta.uniprot.org/

  13. How is it built?

  14. PIR – Protein Information Resource Integrated Protein Literature, Information and Knowledge Protein Family Classification System Integrated Protein Knowledgebase

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