1. Center for Biologisk Sekvensanalyse Nikolaj Blom Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark nikob@cbs.dtu.dk ”Resources of Biomolecular Data: Sequences, Structures and Functionality” PhD course #27803

2. Center for Biologisk Sekvensanalyse Outline Magnitudes and Scales Resources: Data Sources & Tools Primary DNA sources Sequence Repositories Structure Repositories Functional Categorization Integration of Databases The Human Genome Genome Browsers Prediction Tools Evaluation of Prediction Servers Starting points Link collections

3. Center for Biologisk Sekvensanalyse Resources: Sources & Tools There is A LOT OF biomolecular databases/sources A LOT OF overlap of information/redundancy A LOT OF TOOLS Personal picks/preferences User-friendliness Update intervals Curation efforts / error correction Linkage to other DBs

4. Center for Biologisk Sekvensanalyse Faster than Moore’s law...

5. Center for Biologisk Sekvensanalyse Human Genome Published HUGO: Nature, 15.feb.2001 Celera: Science, 16.feb.2001

6. Center for Biologisk Sekvensanalyse Magnitudes and Scales Human genome 3,200,000,000 bp Single basepair  full genome is 9 orders of magnitude Genome = Football field: ~3 billion leaves of grass Single base A T G C (or SNP) = 1 leaf of grass Genome browsing Zooming from whole stadium to single leaf

7. Center for Biologisk Sekvensanalyse How we got the sequence Sanger chain termination method

8. Center for Biologisk Sekvensanalyse Primary DNA sources Trace files repositories Single read: 500-1000 bp (~golf ball size / jig saw puzzle) Variable quality WashU-Merck Human EST Project / Trace files ”Base-calling” non-trivial

9. Center for Biologisk Sekvensanalyse Assembly is Non-trivial!

10. Center for Biologisk Sekvensanalyse Sequence repositories - GenBank et al. GenBank / EMBL / DDBJ Highly redundant (many versions of same gene) Cross-updated daily Version history is recorded Previous sequence records can be retrieved Contigs/HTGS (100-200 kb) finishing at different stages Draft  Finished Includes genomic DNA, cDNA, ESTs, translated peptides

11. Center for Biologisk Sekvensanalyse Non-redundant and Curated databases Non-redundant Manual or automatic curation DNA RefSeq (NCBI; semi-automated) Ensembl gene index (automated) Protein RefSeq (NCBI; semi-automated) TrEMBL (EMBL; automated)

12. Center for Biologisk Sekvensanalyse Curated database: UniProt/SwissProt SIB - Swiss Institute of Bioinformatics Protein Knowledgebase / Sequence Database Highly curated Experimental evidence evaluated (e.g. modifications) All 80,000 entries checked by Amos Bairoch himself ;-) ExPASy - Expert Protein Analysis System Proteomics tools: links + local servers

13. Center for Biologisk Sekvensanalyse Structure databases / Protein Data Bank (PDB) X-ray, NMR biomolecular structures Protein Data Bank (PDB) >22,000 structures (April 2003) http://www.rcsb.org/pdb/

14. Center for Biologisk Sekvensanalyse Functional Categorization Gene Ontology (GO) Hierarchical Controlled vocabulary

15. Center for Biologisk Sekvensanalyse Functional Categorization Gene Ontology (GO) http://www.geneontology.org/ http://www.geneontology.org/ Molecular Function - the tasks performed by individual gene products; examples are transcription factor and DNA helicase Biological Process - broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions Cellular Component - subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex

16. Center for Biologisk Sekvensanalyse Integration of databases - Webs of web- sites Links, links, links... SRS = Sequence Retrieval System Powerful, complex query language BioDAS – Distributed Annotation System http://srs.ebi.ac.uk/

17. Center for Biologisk Sekvensanalyse For ’my gene’, how do I: Get an overview of the sequence information known? (GeneCards) Examine the ’Genome Neighbourhood’? (Genome Browsers) Predict protein post-translational modifications (PTMs)? (Prediction servers) (Evaluate the value of predicted features)

18. Center for Biologisk Sekvensanalyse GeneCards http://nciarray.nci.nih.gov/cards/ http://nciarray.nci.nih.gov/cards/

19. Center for Biologisk Sekvensanalyse GeneCards-II

20. Center for Biologisk Sekvensanalyse GeneCards-III

21. Center for Biologisk Sekvensanalyse GeneCards-IV

22. Center for Biologisk Sekvensanalyse GeneCards-V

23. Center for Biologisk Sekvensanalyse Genetic/Medical Information OMIM, Online Mendelian Inheritance in Man (NCBI) The OMIM database is a catalog of human genes and genetic disorders >13,000 entries (April, 2002) Examples: cystic fibrosis, prions, amyloid precursor protein Condensed, highly curated descriptions of genetics/disease/animal models/references

24. Center for Biologisk Sekvensanalyse OMIM-I (http://www3.ncbi.nlm.nih.gov/Omim/)http://www3.ncbi.nlm.nih.gov/Omim/

25. Center for Biologisk Sekvensanalyse OMIM-II

26. Center for Biologisk Sekvensanalyse OMIM-III

27. Center for Biologisk Sekvensanalyse For ’my gene’, how do I: Get an overview of the sequence information known? (GeneCards) Examine the ’Genome Neighbourhood’? (Genome Browsers) Predict protein post-translational modifications (PTMs)? (Prediction servers) (Evaluate the value of predicted features)

28. Center for Biologisk Sekvensanalyse Genome Browsing Three public Open access Use same genome build/assembly NCBI (U.S.) UCSC (Santa Cruz, U.S.) EnsEmbl (EBI, EU) One private Restricted, commercial Academic, free usage: 1 Mbase/week Proprietary assembly Celera Genomics (U.S.)

29. Center for Biologisk Sekvensanalyse Celera Human/Mouse Genomes

30. Center for Biologisk Sekvensanalyse Genome Browsers - Portals to the Genomic World NCBI – National Center for Biotechnology Information (U.S.) http://www.ncbi.nlm.nih.gov/Genomes/index. html http://www.ncbi.nlm.nih.gov/Genomes/index. html UCSC – Univ. California – Santa Cruz (U.S.) http://genome.ucsc.edu/ EnsEmbl – European Molecular Biology Laboratory (E.U.) http://www.ensembl.org/

31. Center for Biologisk Sekvensanalyse NCBI

32. Center for Biologisk Sekvensanalyse NCBI

33. Center for Biologisk Sekvensanalyse UCSC – Genome Browser

34. Center for Biologisk Sekvensanalyse UCSC – Genome Browser II

35. Center for Biologisk Sekvensanalyse

36. EnsEmbl – Genome Browser

37. Center for Biologisk Sekvensanalyse EnsEmbl – Genome Browser

38. Center for Biologisk Sekvensanalyse EnsEmbl – Genome Browser

39. Center for Biologisk Sekvensanalyse EnsEmbl – Genome Browser

40. Center for Biologisk Sekvensanalyse EnsEmbl – Genome Browser

41. Center for Biologisk Sekvensanalyse EnsEmbl – Genome Browser

42. Center for Biologisk Sekvensanalyse For ’my gene’, how do I: Get an overview of the sequence information known? (GeneCards) Examine the ’Genome Neighbourhood’? (Genome Browsers) Predict protein post-translational modifications (PTMs) or Gene Structure? (Prediction servers)...and evaluate the reliability of prediction methods

43. Center for Biologisk Sekvensanalyse CBS Services/Toolbox http://www.cbs.dtu.dk/services/ http://www.cbs.dtu.dk/services/

44. Center for Biologisk Sekvensanalyse

45. NetPhos – a prediction server http://www.cbs.dtu.dk/services/NetPhos/

46. Center for Biologisk Sekvensanalyse NetPhos – a prediction server

47. Center for Biologisk Sekvensanalyse Evaluating Prediction Servers Performance on independent/cross- validated data presented? Published in peer-reviewed journal? Cited by others? Science Citation Index Linked to from credible web sites? Google Page-rank ”link:URL” search

48. Center for Biologisk Sekvensanalyse Evaluating Prediction Servers

49. Center for Biologisk Sekvensanalyse 2can Bioinformatics Education At EBI – European Bioinformatics Institute http://www.ebi.ac.uk/2 can/index.html Tutorials, resource links, etc.

50. Center for Biologisk Sekvensanalyse Starting Points General Bioinformatics NCBI, National Center for Biotechnology Information, U.S. EBI, European Bioinformatics Institute Prediction Tools CBS, DK Expasy (Protein analysis), Switzerland

51. Center for Biologisk Sekvensanalyse Dynamic Resources Pros Includes most recent developments Updated regularly User interface improves(usually) Cons Difficult to keep pace Tutorials and lectures hard to recycle ;-( Difficult to use at irregular intervals

52. Center for Biologisk Sekvensanalyse Genome Browsers - Portals to the Genomic World Three main entry points: NCBI, UCSC, EnsEmbl Essentially contain same information High degree of linking to secondary databases Advisable to become familiar with only one genome browser Learn to navigate and make queries GeneCards and OMIM well suited for getting a quick overview of a gene of interest

53. Center for Biologisk Sekvensanalyse Prediction Servers Evaluate scientific ’soundness’ Look for indications of quality (citations, etc.) Remember that prediction servers provide...well, predictions!

54. Center for Biologisk Sekvensanalyse The End