Obtaining genomic data from the UCSC database using table browser queries

This UCSC table browser allows execution of complex database queries without knowledge of database query languages.

Open the UCSC browser

select the "Genomes" link.

Select the May 2004 Human assembly and enter: 

chr4:134,416,924-134,488,579 

in the "position or search term" window, click submit.

Click the "Tables" link in the upper blue bar to open up a Table Browser page.

The Table Browser

• Note the organism and assembly controls (red box)
• Note the data type controls (blue box)
• Note the region selection option

• The data type controls are associated with different browser tracks

-Set group to "Genes and Gene Prediction Tracks", track to "Known Genes", and table to "knownGene".
-Restrict region to chr4:134416924-134488579
-locate the output format menu and select "GTF - gene transfer format". Note the other options.
-Click the "summary/statistics" button at the bottom of the page. 
 This provides details about your query results and can be very useful. 
 You should get and item count of 3.
-Return to the Table Browser and click the "get output" button. 
 A text file will appear on your screen that describes the structure of the known genes in this region. 
 This file can be saved and used later. 

• A precomputed version of this file is HERE.

Perform the same set of operations to obtain similar data for ESTs in the region. 
How many human ESTs are in the region.

• A precomputed version of this file is HERE.