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Demo: Exploiting the UCSC Genome Browser

Demo: Exploiting the UCSC Genome Browser

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Demo: Exploiting the UCSC Genome Browser

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

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

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

  4. Configure Tracks

  5. Spliced ESTs

  6. Genome Gateway Help/User’s Guide

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

  8. Table Browser:Tabular output of simple repeats in QARS

  9. Get all fields 1 2 Tabular output of simple repeats in QARS

  10. 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

  11. Go to the Table Browser and choose the Human assembly from July 2003

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

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

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

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

  16. 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

  17. 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

  18. 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

  19. 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?

  20. . . . Data Downloads http://genome.ucsc.edu/downloads.html

  21. Example: simpleRepeats table

  22. 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