Demo: Exploiting the UCSC Genome Browser

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Demo Exploiting the UCSC Genome Browser

• Stefanie Butland
• UBC Bioinformatics Centre
• butland_at_bioinformatics.ubc.ca

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UCSC Genome Gateway Structure
Custom tracks
Genome browser
Table browser
Your sequence
BLAT
Family browser
Downloadable files http//genome.ucsc.edu/download
s.html
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http//genome.ucsc.edu/cgi-bin/hgGateway
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Configure Tracks
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Spliced ESTs
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Genome Gateway Help/Users Guide
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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

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Table BrowserTabular output of simple repeats
in QARS
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Tabular output of simple repeats in QARS
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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 chr41-25,000,000

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

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

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• for Position, enter chr41-25000000 and click
  Advanced query
• under Select Output Format for knownGene, choose
  Custom Track and scroll down the page

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

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

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• 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

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• 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

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• 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

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• 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?

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Data Downloads http//genome.ucsc.edu/downloads.ht
ml
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Example simpleRepeats table
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Other Examples

• For other examples to work through, see
• Creating custom annotation tracks section of
  the Users Guide http//genome.ucsc.edu/goldenPath
  /help/hgTracksHelp.html
• Table Browser paper, Karolchik et al (2004) NAR
  32D493-D496