1. Visualization of genomic data Genome browsers

2. UCSC browser Ensembl browser Others ? Survey

3. UCSC genome browser Basic functionalities used in exercise 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. Visualization of genomic data Genome browsers

5. Genome browsers Visualization of a gene >chr5:123.004.678-125.345.112 ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA Chr5123.004.678 123.404.678124.987.012125.345.112 Flat files / tab files

6. Genome browsers Why graphic Display ? Why is a graphic display better than Flat files / tab files A graphic display is compact Meta data available i.e. Support information about a gene Experimental evidence like EST Predicted gene structures SNP information Links to many databases In short much data about a gene is gathered is one place and can be viewed easily.

7. Genome browsers Visualization of a gene (Ensembl)

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

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. 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

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 genome Browser

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

17. Logo Plot Information Content IC = -H(p) + log 2 (4) =  a p a log 2 p a + 2 The Information content is calculated from a multiple sequence alignment. Result is a graphical visualization of sequence conservation where: Total height at a position is the Information Content Height of single letter is proportional to the frequency of that letter Mutiple alignment of 3 protein sequences: Seq1: A L R K P Q R T Seq2: A V R H I L L I Seq3: A I K V H N N T Pos1: I = -[1*log 2 (1)]+ 4.32 = log 2 (20) = 4.32 Pos2: I = -[1/3*log 2 (1/3)+ 1/3*log 2 (1/3)+ 1/3*log 2 (1/3)] + 4.32 = 2.73 Pos3: I = -[2/3*log 2 (2/3)+ 1/3*log 2 (1/3) + 4.32 = 3.38

18. Logo Plot Exon

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. Genome browsers

25. BLAT genome Browser Center & zoom

26. Forward/reverse direction Selected number of tracks

27. BLAT genome Browser Sequence Orthologs

28. “klick”

29. BLAT genome Browser Sequence Orthologs

32. SNPs

34. 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