Gaggle Components
Data Standards

Gaggle Genome Browser

Getting Started

The genome browser is designed to be as simple to use as possible. Getting started is as easy as selecting an organism. We used Java web start to launch the application by clicking a link. Go ahead and launch the an empty genome browser by clicking on the link below.

Launch genome browser

Once the program starts, select File | New Dataset. This will bring up a menu of organisms for which there is data in the UCSC genome browser or its microbial sister project.

We'll use E. coli as our example organism. Since nobody knows how to spell "Escherichia", start typing "coli" instead. The menu should narrow your search down to several strains of E. coli. Select Escherichia coli str. K12 substr. W3110 using the down-arrow and enter keys or by double-clicking in the list.

Press enter and the genome browser will download the locations of genes, tRNAs, and ribosomal RNAs and plot those along a horizontal axis. Your screen should look something like the figure below.

Behind the scenes, the software constructed a sqlite database. This file, named after the selected organism, will be located in a directory called hbgb (the browser's nickname is heebieGB) in the conventional user document directory of your operating system. The database was populated with a genome track which contains features that represent protein coding regions and RNAs.

Use the hand tool to drag the viewport right and left. Or try zooming out to view a larger section of the E. coli genome.

Where to go from here

The next thing you'll likely want to do is import data. Or, you may want more details on creating a new project.


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