http://creativecommons.org/licenses/by-sa/2.0/ Lab 7.2

Exploiting the UCSC Genome Gateway Stefanie Butland February 21, 2004 Exploiting the UCSC Genome Gateway Stefanie Butland UBC Bioinformatics Centre butland@bioinformatics.ubc.ca Lab 7.2 (c) 2005 CGDN

UCSC Genome Gateway Structure Stefanie Butland February 21, 2004 UCSC Genome Gateway Structure Custom tracks Genome browser Table browser Database Your sequence Gene sorter BLAT in silico PCR Proteome browser Genome browser creates each line of its graphical annotation image by querying the corresponding table in the database. Survey: how many have used UCSC browser, BLAT, Table browser, custom track, downloaded data, mySQL server? Downloadable data files Public MySQL server Lab 7.2 (c) 2005 CGDN

http://genome.ucsc.edu/cgi-bin/hgGateway Stefanie Butland February 21, 2004 Last year there were 9 genomes; now 25 incl a couple of comparative genomic sequencing projects. No plants. What use if my genome isn’t there? Look for related genome Lab 7.2 (c) 2005 CGDN

Lab 7.2

Browse Human genome Lab 7.2

Lab 7.2

Configure Tracks – Spliced ESTs and Simple Repeats Lab 7.2

Spliced ESTs cf Acembly Simple Repeats Stefanie Butland February 21, 2004 Spliced ESTs cf Acembly Possible evidence for alt splicing; compare this with Acembly predictions Simple Repeats Lab 7.2 (c) 2005 CGDN

Genome Gateway Help/User’s Guide Lab 7.2

Worked Examples Genome Browser – instructor only Stefanie Butland February 21, 2004 Worked Examples Genome Browser – instructor only Glutaminyl-tRNA Synthetase (QARS) gene structure and sequence (see 7.2 notes for guide) BLAT and in silico PCR of primers (see 7.2 notes for guide) Table Browser – walk through together Locations of simple repeats in QARS Table Browser and Custom Tracks – on your own Trinucleotide repeats within genes on chromosome 4 Walk thru QARS tracks, gene structure Lab 7.2 (c) 2005 CGDN

Table Browser: Tabular output of simple repeats in QARS Lab 7.2

Tabular output of simple repeats in QARS Lab 7.2

Custom Tracks generated by the Table Browser Research Question: Which trinucleotide repeats in the first 25 Mb of chromosome 4 are contained within known genes? An answer to this question can be found in the intersection of the Simple Repeats table (limited to repeat period = 3) with the Known Genes table in the region chr4:1-25,000,000 Lab 7.2

Click Describe Table Schema for info on Simple Repeats content Go to the Table Browser and choose Variation and Repeats: Simple Repeats track Click Describe Table Schema for info on Simple Repeats content Lab 7.2

Simple Repeats table schema Lab 7.2

for Position, enter ‘chr4:1-25000000’ and choose create filter Lab 7.2

Set period = 3 for trinucleotide repeats Lab 7.2

Select create intersection and choose Genes and Gene Prediction Tracks: Known Genes Lab 7.2

Choose custom track output format and click Get Output Lab 7.2

Choose Genome Browser option Lab 7.2

Observe new track with 5 annotations in the region Lab 7.2

Centre on 1st trf and note that it overlaps with gene for HD – Huntington disease, which is caused by trinucleotide repeat expansion Lab 7.2

UCSC Proteome Browser Lab 7.2

Lab 7.2

Lab 7.2

Data Downloads http://genome.ucsc.edu/downloads.html . . . Lab 7.2

Example: simpleRepeats table Lab 7.2

Public MySQL Server See the Data and Downloads FAQ: Direct MySQL access to data http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Command from local MySQL client: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A Lab 7.2

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 Lab 7.2