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Demo: Exploiting the UCSC Genome Browser. Stefanie Butland UBC Bioinformatics Centre [email protected] Database. UCSC Genome Gateway Structure. Custom tracks. Genome browser. Table browser. Your sequence. BLAT. Family browser. Downloadable files

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Demo exploiting the ucsc genome browser l.jpg

Demo: Exploiting the UCSC Genome Browser

Stefanie Butland

UBC Bioinformatics Centre

[email protected]


Ucsc genome gateway structure l.jpg

Database

UCSC Genome Gateway Structure

Custom tracks

Genome browser

Table browser

Your

sequence

BLAT

Family browser

Downloadable files

http://genome.ucsc.edu/downloads.html






Worked examples l.jpg
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


Table browser tabular output of simple repeats in qars l.jpg
Table Browser:Tabular output of simple repeats in QARS


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Get all fields

1

2

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 chr4:1-25,000,000



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Research Question: turn the Simple Repeats track on in pack mode to view these

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?


Data downloads http genome ucsc edu downloads html l.jpg

. . . turn the Simple Repeats track on in pack mode to view these

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


Example simplerepeats table l.jpg
Example: simpleRepeats table turn the Simple Repeats track on in pack mode to view these


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Other Examples turn the Simple Repeats track on in pack mode to view these

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


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