1. Visualization of genomic data Genome browsers

2. How many have used a genome browser ? UCSC browser ? Ensembl browser ? Others ? survey

3. Visualization of genomic data Genome browsers

4. 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

5. Genome browsers Visualization of a gene (Ensembl)

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

7. Genome browsers

9. 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

10. UCSC genome browser Basic functionalities Finding a gene by name by sequence Gene structure Sequence orthologues Single Nucleotide Polymorphisms Gene Sorter - sort according to expression, homology... Custom tracks

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 RNA/DNA 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. BLAT genome Browser ”Details” Donor site | Acceptor site exon.... G | GT...intron...AG | exon...

19. Blat genome Browser

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

21. BLAT genome Browser Center & zoom

22. Forward/reverse direction Selected number of tracks

23. BLAT genome Browser Sequence Orthologs

24. “klick”

25. BLAT genome Browser Sequence Orthologs

28. SNPs

30. Chromosomal locus A locus is a physical location on a chromosome p the ‘short arm’ q the ‘long arm’ A locus range may describe a location of a gene 22q11.21-q11.23 22q12.2 Chromosome22 Armq Band12 Sub-band2

31. Chromosomal locus Searching with gene name

32. Chromosomal locus Searching with locus range

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

34. Custom tracks

36. Exercise 1.Basic understanding of the graphics 2.Effect of Single Nucleotide Polymorphisms (SNPs) 3.Finding Orthologue genes 4.Identify chromosomal locus for a gene