1. Visualization of genomic data Genome browsers

2. UCSC browser Ensembl browser Others ? Survey

3. UCSC genome browser Basic functionalities Finding a gene by name by sequence Gene structure Orthologues – i.e. functional homolog in other organisms SNP’s - Single Nucleotide Polymorphisms Several other functionalities Gene Sorter - sort according to expression, homology, in situ images of genes in different tissues Custom tracks – upload your own data

4. UCSC genome browser http://genome.ucsc.edu/ Easy to use Often updates, but not as often as Ensembl upload of personal tracks Ensembl browser http://www.ensembl.org/index.html Less easy to use Maintained/updated by several people Gbrowser http://www.gmod.org/GBrowse Genome browsers

5. Visualization of genomic data Genome browsers

6. Genome browsers Visualization of a gene >sequence ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA Chr5123.004.678 123.404.678124.987.012125.345.112 Flat files / tab files Exon Intron

7. Genome browsers Visualization of a gene (Ensembl)

8. Genome browsers Visualization of a gene (UCSC) Exon Intron UTR Header

9. Genome browsers

11. BLAT genome Browser http://genome.ucsc.edu//

12. BLAT genome Browser Using a search term or position eg Chr1:10,234-11,567

13. BLAT genome Browser http://genome.ucsc.edu/

14. BLAT genome Browser Using a protein or DNA sequence

15. BLAT Blast Like Alignment Tool BLAT (2002) Very fast searches (MySQL database) Handle introns in genomic alignments Data for more that 30 genomes (human, mouse, rat…) Exon Intron Exon Splice sites

16. Blat genome Browser

17. BLAT genome Browser ”Details” Correct splice site ?

18. Splice sites

19. BLAT genome Browser ”Details” Correct splice site ?

20. BLAT genome Browser ”Details” Donor site | Acceptor site exon.... G | GT...intron...AG | exon...

21. Blat genome Browser

22. BLAT genome Browser ”Browser” Base, Center & Zoom Known genes Predictions RNA EST Conservation Expression

23. BLAT genome Browser Center & zoom

24. Forward/reverse direction Selected number of tracks

25. BLAT genome Browser Sequence Orthologs

26. “klick”

27. BLAT genome Browser Sequence Orthologs

30. SNPs

32. Gene Sorter

33. Gene Sorter - homology Closest homologues

34. Custom tracks Upload your personal data Share data with colleagues Data need to be related to a reference organism

35. Custom tracks

37. Exercise 1.Basic understanding of the graphics 2.Effect of Single Nucleotide Polymorphisms (SNPs) 3.Finding Orthologue genes http://www.cbs.dtu.dk/courses/humanbio/2009/exercises/ExGenomeBrowser/ExGenomeBrowser.pdf