1.
Lab 7.2

2. Exploiting the UCSC Genome Gateway
Stefanie Butland
February 21, 2004
Exploiting the UCSC Genome Gateway
Stefanie Butland
UBC Bioinformatics Centre
Lab 7.2
(c) 2005 CGDN

3. UCSC Genome Gateway Structure
Stefanie Butland
February 21, 2004
UCSC Genome Gateway Structure
Custom tracks
Genome browser
Table browser
Database
Your
sequence
Gene sorter
BLAT
in silico PCR
Proteome browser
Genome browser creates each line of its graphical annotation image by querying the corresponding table in the database.
Survey: how many have used UCSC browser, BLAT, Table browser, custom track, downloaded data, mySQL server?
Downloadable data files
Public MySQL server
Lab 7.2
(c) 2005 CGDN

4. http://genome.ucsc.edu/cgi-bin/hgGateway Stefanie Butland
February 21, 2004
Last year there were 9 genomes; now 25 incl a couple of comparative genomic sequencing projects. No plants. What use if my genome isn’t there? Look for related genome
Lab 7.2
(c) 2005 CGDN

5. Lab 7.2

6. Browse Human genome
Lab 7.2

7. Lab 7.2

8. Configure Tracks – Spliced ESTs and Simple Repeats
Lab 7.2

9. Spliced ESTs cf Acembly Simple Repeats Stefanie Butland
February 21, 2004
Spliced ESTs
cf Acembly
Possible evidence for alt splicing; compare this with Acembly predictions
Simple Repeats
Lab 7.2
(c) 2005 CGDN

10. Genome Gateway Help/User’s Guide
Lab 7.2

11. Worked Examples Genome Browser – instructor only
Stefanie Butland
February 21, 2004
Worked Examples
Genome Browser – instructor only
Glutaminyl-tRNA Synthetase (QARS) gene structure and sequence (see 7.2 notes for guide)
BLAT and in silico PCR of primers (see 7.2 notes for guide)
Table Browser – walk through together
Locations of simple repeats in QARS
Table Browser and Custom Tracks – on your own
Trinucleotide repeats within genes on chromosome 4
Walk thru QARS tracks, gene structure
Lab 7.2
(c) 2005 CGDN

12. Table Browser: Tabular output of simple repeats in QARS
Lab 7.2

13. Tabular output of simple repeats in QARS
Lab 7.2

14. Custom Tracks generated by the Table Browser
Research Question: Which trinucleotide repeats in the first 25 Mb of chromosome 4 are contained within known genes?
An answer to this question can be found in the intersection of the Simple Repeats table (limited to repeat period = 3) with the Known Genes table in the region chr4:1-25,000,000
Lab 7.2

15. Click Describe Table Schema for info on Simple Repeats content
Go to the Table Browser and choose Variation and Repeats: Simple Repeats track
Click Describe Table Schema for info on Simple Repeats content
Lab 7.2

16. Simple Repeats table schema
Lab 7.2

17. for Position, enter ‘chr4:1-25000000’ and choose create filter
Lab 7.2

18. Set period = 3 for trinucleotide repeats
Lab 7.2

19. Select create intersection and choose Genes and Gene Prediction Tracks: Known Genes
Lab 7.2

20. Choose custom track output format and click Get Output
Lab 7.2

21. Choose Genome Browser option
Lab 7.2

22. Observe new track with 5 annotations in the region
Lab 7.2

23. Centre on 1st trf and note that it overlaps with gene for HD – Huntington disease, which is caused by trinucleotide repeat expansion
Lab 7.2

24. UCSC Proteome Browser
Lab 7.2

25. Lab 7.2

26. Lab 7.2

27. Data Downloads http://genome.ucsc.edu/downloads.html
. . .
Lab 7.2

28. Example: simpleRepeats table
Lab 7.2

29. Public MySQL Server
See the Data and Downloads FAQ: Direct MySQL access to data
Command from local MySQL client:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
Lab 7.2

30. Other Examples For other examples to work through, see:
“Creating custom annotation tracks” section of the User’s Guide
Table Browser paper, Karolchik et al (2004) NAR 32:D493-D496
Lab 7.2