Web site: bioinfo.weizmann.ac.il/ws Mailing list: bioinfo.weizmann.ac.il/announce Contact: Vered.Caspi@weizmann.ac.il

1. Web site: http://bioinfo.weizmann.ac.il/ws Mailing list: http://bioinfo.weizmann.ac.il/announce Contact: Vered.Caspi@weizmann.ac.il

2. Genomic Databases and Analysis Tools 09:00-09:45 Vered Chalifa-Caspi Genomic Databases: from primary DNA sequence to gene function 09:45-11:00 Shifra Ben-Dor States of the human and mouse genomes 11:00-11:15 Coffee Break

3. 11:15-12:15 Nili Avidan Web-based analysis and annotation tools 12:15-13:00 Marilyn Safran GeneCards: a database of human genes, their products and their involvement in diseases 13:00-14:00 Lunch Break 14:00-16:00 Hands-on at Ebner Computer Classroom

4. Genomic Databases:from primary DNA sequenceto gene function Vered Chalifa-Caspi Bioinformatics and Biological Computing Unit Biological Services Department Weizmann Institute of Science

7. Starting Pointsfor Navigation

8. http://www.ncbi.nlm.nih.gov

9. http://www.ebi.ac.uk/

10. http://dapsas.weizmann.ac.il http://bioinfo.weizmann.ac.il

11. Genomic Databases • Genomic Sequences • mRNA Sequences • Genome Viewers • Gene Databases • Genetic Variation • Gene Expression • Protein Databases • Protein Classification • Pathways

12. Genomic Sequences

13. Genomic sequences • All sequences are archived in GenBank/EMBL/DDBJ • Genomic sequences:- unfinished clones.- finished clones.- clone contigs.- entire chromosomes.- entire genomes.

15. mRNA Sequences

16. mRNA sequences • Full mRNA sequences • Expressed Sequence Tags (ESTs) • EST clusters • EST assemblies • Predicted genes

17. Genomic, mRNA and EST sequences

19. Genome Viewers

20. By integrating map and sequence information, a whole-genome view can be constructed Annotation Gene A Predicted gene K Gene B

21. Resources for whole human genome sequence assembly 1. Human Genome Project Working Draft at the University of California at Santa Cruz 2. Ensembl EMBL - EBI and the Sanger Institute 3. MapViewer at NCBI

22. University of Californiaat Santa Cruz http://genome.cse.ucsc.edu/

24. Gene Databases

28. Genetic Variation

29. http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html

30. Search for BRCA1

31. BRCA1 - Nucleotide substitutions (missense / nonsense) . . .

32. http://www.geneclinics.org/

34. http://ariel.ucs.unimelb.edu.au:80/~cotton/glsdb.htm

37. http://www.ncbi.nlm.nih.gov/SNP/

38. dbSNP A central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.

40. http://hgvbase.cgb.ki.se/

41. Gene Expression

42. Edgar et al. Nucleic Acids Research, 2002, Vol. 30, No. 1 207-210 http://nar.oupjournals.org/cgi/content/full/30/1/207/GKF066TB1

43. http://www.ncbi.nlm.nih.gov/geo/

44. http://www.hugeindex.org

45. Protein Databases

46. http://www.expasy.ch/sprot/

48. http://www.ebi.ac.uk/interpro/ Integrated resource of Protein Families, Domains and Sites. Unifies signature databases (PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs) Useful for: - Identifying distant relationships in novel sequences - Predicting protein function and structure. - Large-scale genome annotation.

49. Protein Classification

50. http://www.geneontology.org/