1. Visualization of genomic data
19-Nov-18
Genome browsers 
Visualization of genomic data

2. 19-Nov-18
Survey 
UCSC browser
Ensembl browser
Others ?

3. UCSC genome browser Basic functionalities
19-Nov-18
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. Genome browsers  UCSC genome browser http://genome.ucsc.edu/
19-Nov-18
Genome browsers 
UCSC genome browser
Easy to use
Often updates, but not as often as Ensembl
upload of personal tracks
Ensembl browser
Less easy to use
Maintained/updated by several people
Gbrowser

5. Visualization of genomic data
19-Nov-18
Genome browsers 
Visualization of genomic data

6. Genome browsers Visualization of a gene
19-Nov-18
Genome browsers Visualization of a gene 
Flat files / tab files
>sequence
ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC
GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG
AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC
TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC
ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT
GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG
GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC
GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT
AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA
Exon
Intron
Exon
Chr

7. Genome browsers Visualization of a gene (Ensembl)
19-Nov-18
Genome browsers Visualization of a gene (Ensembl) 

8. Genome browsers Visualization of a gene (UCSC)
19-Nov-18
Genome browsers Visualization of a gene (UCSC) 
Header
Exon Intron UTR

9. 19-Nov-18
Genome browsers 

10. 19-Nov-18
Genome browsers 

11. 19-Nov-18
BLAT genome Browser

12. 19-Nov-18
BLAT genome Browser
Using a search term or position eg Chr1:10,234-11,567

13. 19-Nov-18
BLAT genome Browser

14. 19-Nov-18
BLAT genome Browser
Using a protein or DNA sequence

15. BLAT Blast Like Alignment Tool
19-Nov-18
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. 19-Nov-18
Blat genome Browser

17. BLAT genome Browser ”Details”
19-Nov-18
BLAT genome Browser ”Details”
Correct splice site ?

18. 19-Nov-18
Splice sites

19. BLAT genome Browser ”Details”
19-Nov-18
BLAT genome Browser ”Details”
Correct splice site ?

20. BLAT genome Browser ”Details”
19-Nov-18
BLAT genome Browser ”Details”
Donor site | Acceptor site
exon... . G | GT ...intron ...AG | exon...

21. 19-Nov-18
Blat genome Browser

22. BLAT genome Browser ”Browser”
19-Nov-18
BLAT genome Browser ”Browser”
Base,
Center &
Zoom
Known genes
Predictions
RNA
EST
Expression
Conservation

23. BLAT genome Browser Center & zoom
19-Nov-18
BLAT genome Browser Center & zoom

24. BLAT genome Browser Center & zoom
19-Nov-18
BLAT genome Browser Center & zoom
Selected number of tracks
Forward/reverse direction

25. BLAT genome Browser Sequence Orthologs
19-Nov-18
BLAT genome Browser Sequence Orthologs

26. BLAT genome Browser Sequence Orthologs
19-Nov-18
BLAT genome Browser Sequence Orthologs
“klick”

27. BLAT genome Browser Sequence Orthologs
19-Nov-18
BLAT genome Browser Sequence Orthologs

28. BLAT genome Browser Sequence Orthologs
19-Nov-18
BLAT genome Browser Sequence Orthologs

29. BLAT genome Browser Sequence Orthologs
19-Nov-18
BLAT genome Browser Sequence Orthologs

30. 19-Nov-18
SNPs

31. 19-Nov-18
SNPs

32. 19-Nov-18
Gene Sorter

33. 19-Nov-18
Gene Sorter - homology
Closest homologues

34. Custom tracks Upload your personal data Share data with colleagues
19-Nov-18
Custom tracks
Upload your personal data
Share data with colleagues
Data need to be related to a reference organism

35. 19-Nov-18
Custom tracks

36. 19-Nov-18
Custom tracks

37. Exercise Basic understanding of the graphics
19-Nov-18
Exercise
Basic understanding of the graphics
Effect of Single Nucleotide Polymorphisms (SNPs)
Finding Orthologue genes