Transcript Information Encoding in Biological Molecules: DNA and

Demo: Exploiting the UCSC
Genome Browser
Stefanie Butland
UBC Bioinformatics Centre
[email protected]
Lab 3.4
1
UCSC Genome Gateway Structure
Custom tracks
Genome
browser
Table browser
Your
sequence
BLAT
Database
Family
browser
Downloadable files
http://genome.ucsc.edu/downloads.html
Lab 3.4
2
http://genome.ucsc.edu/cgi-bin/hgGateway
Lab 3.4
3
Lab 3.4
4
Lab 3.4
5
Lab 3.4
6
Configure Tracks
Lab 3.4
7
Spliced ESTs
Lab 3.4
8
Genome Gateway Help/User’s Guide
Lab 3.4
9
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
Lab 3.4
10
Table Browser:
Tabular output of simple repeats in QARS
Lab 3.4
11
Lab 3.4
12
Lab 3.4
13
2
Get all fields
1
Tabular output of simple
repeats in QARS
Lab 3.4
14
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
Lab 3.4
15
• Go to the Table Browser and choose the Human assembly from
July 2003
Lab 3.4
16
• Choose Browser Tracks - Known Genes, and click Describe
table for info on Known Genes content
Lab 3.4
17
• for Position, enter ‘chr4:1-25000000’ and click Advanced query…
• under Select Output Format for knownGene, choose Custom Track…
and scroll down the page
Lab 3.4
18
• under (Optional) Intersect Results with Another Table, choose
Browser Tracks – Simple Repeats, and click Intersect Results
Lab 3.4
19
• under (Optional) Filter simpleRepeat Records by Field Values,
select period is = 3 and click Custom Track...
Lab 3.4
20
• 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
Lab 3.4
21
• 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
Lab 3.4
22
• 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
Lab 3.4
23
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?
Lab 3.4
24
Data Downloads
...
http://genome.ucsc.edu/downloads.html
Lab 3.4
25
Example: simpleRepeats table
Lab 3.4
26
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
•
Lab 3.4
Table Browser paper, Karolchik et al (2004)
NAR 32:D493-D496
27