1. Lab 3.41 Demo: Exploiting the UCSC Genome Browser Stefanie Butland UBC Bioinformatics Centre butland@bioinformatics.ubc.ca

2. Lab 3.42 UCSC Genome Gateway Structure Downloadable files http://genome.ucsc.edu/downloads.html Table browser Genome browser Database Custom tracks Family browser Your sequence BLAT

3. Lab 3.43 http://genome.ucsc.edu/cgi-bin/hgGateway

4. Lab 3.44

5. 5

6. 6

7. 7 Configure Tracks

8. Lab 3.48 Spliced ESTs

9. Lab 3.49 Genome Gateway Help/User’s Guide

10. Lab 3.410 Worked Examples Genome Browser 1.Glutaminyl-tRNA Synthetase (QARS) gene structure and sequence (see Demo 3.4 notes for guide) 2.BLAT of Factor VIII primers (see Demo 3.4 notes for guide ) Table Browser 3.Locations of simple repeats in QARS Table Browser and Custom Tracks 4.Known genes on chromosome 4 that contain trinucleotide repeats

11. Lab 3.411 Table Browser: Tabular output of simple repeats in QARS

12. Lab 3.412

13. Lab 3.413

14. Lab 3.414 Get all fields 1 2 Tabular output of simple repeats in QARS

15. Lab 3.415 Custom Tracks generated by the Table Browser Research Question: Which known genes in the first 25 Mb of chromosome 4 contain trinucleotide repeats? An answer to this question can be found in the intersection of the Known Genes table with the Simple Repeats table (limited to repeat period = 3) in the region chr4:1-25,000,000

16. Lab 3.416 Go to the Table Browser and choose the Human assembly from July 2003

17. Lab 3.417 Choose Browser Tracks - Known Genes, and click Describe table for info on Known Genes content

18. Lab 3.418 for Position, enter ‘chr4:1-25000000’ and click Advanced query… under Select Output Format for knownGene, choose Custom Track… and scroll down the page

19. Lab 3.419 under (Optional) Intersect Results with Another Table, choose Browser Tracks – Simple Repeats, and click Intersect Results

20. Lab 3.420 under (Optional) Filter simpleRepeat Records by Field Values, select period is = 3 and click Custom Track...

21. Lab 3.421 click Get Custom Track File to view the text output, then go back and click Get Custom Track to view this graphically in the Genome Browser

22. Lab 3.422 click Get Custom Track File to view the text output, then go back and click Get Custom Track to view this graphically in the Genome Browser

23. Lab 3.423 Find a way to zoom in on one of the genes with a repeat and turn the Simple Repeats track on in pack mode to view these

24. Lab 3.424 Research Question: Which known genes in the first 25 Mb of chromosome 4 contain trinucleotide repeats? Related questions: How many genes is this? Conduct the query in reverse - how many trinucleotide repeats are in known genes in the first 25 Mb of chromosome 4. Can you explain the difference between the results of these queries?

25. Lab 3.425 Data Downloads http://genome.ucsc.edu/downloads.html...

26. Lab 3.426 Example: simpleRepeats table

27. Lab 3.427 Other Examples For other examples to work through, see: “Creating custom annotation tracks” section of the User’s Guide http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html Table Browser paper, Karolchik et al (2004) NAR 32:D493-D496