Working with SVA genome browser

 

SVA provides an integrated genome browser, located at a "genome browser" panel:

1. The data for SVA genome browser

The data for the SVA genome browser (saved in a .gbb file) is separate from your project variant data (saved in a .bin file). The path for this .gbb file is specified in your project file (.gsap file) with this field: "[GenomeBrowserBuffer]=" .The genome browser .gbb file can be automatically generated from the supporting databases released with SVA, as long as you specified the "[GenomeBrowserBuffer]=" field in your project.

For you different projects with (1) the same genome build, and (2) the same number of chromosomes, you do not need to re-generate the .gbb file separately for each of these projects during the annotation, and may just use the existing .gbb file and leave the "[GenomeBrowserBufferSwitch]=on" statement. In this case SVA will directly load the existing .gbb genome browser buffer file.

For the whole genome build 36, the size of the corresponding .gbb file is around 1.5GB. For chromosome X only as in the example project, the size of the corresponding .gbb file is around 60MB.

2. Starting SVA genome browser

By default the SVA genome browser is not initiated when you load a project. The status of SVA genome browser is indicated in the status bar at the bottom of the genome browser panel (figures below).

There are several equivalent ways to start SVA genome browser:

[1]. Menu "File -> Start genome browser"

[2]. "Genome browser" button in the main tool bar at the top of the program (figure below)

[3]. An option in the project build window.
[4]. Sometimes if you perform an analysis which requires SVA genome browser, it will start up automatically after asking your permission.

 

3. Navigating in SVA genome browser

The SVA genome browser has to be started first for the navigation system to work. The SVA genome browser provides several navigation options (figure below). In the following table I list these options (top to bottom, left to right):

[1]. Chromosome coordinate navigating
[2] Gene symbol navigating. The drop-down box is pre-set with the gene symbols as in Ensembl build 50_36l, or any updated SVA build you are working with. If it won't let you type in gene symbols, that means the gene symbol is not in the database. You may try an alias.
[3] refSNP navigating. The drop-down box is pre-set with the SNP entry as in Ensembl build 50_36l (dbSNP build 129), or any updated SVA build you are working with. If it won't let you type in the SNP name, that means the SNP is not in the database.
[4] Move/Zoom navigating. There are six buttons (blue buttons at the right) provided, moving or zooming at the step specified in the drop-down box at the left. There buttons are: moving towards smaller coordinate; moving towards larger coordinate; zooming in; zooming out; zooming in by 2-fold; zoom out by 2-fold.

4. Select sections to display

Click on the "Select sections to display" button in the navigation tool bar (figure above), you will see a dialog like this:

This option allows you to select the displayed sections in the SVA genome browser.

5. A real example: search for the Factor VIII gene in the example project

Using the example project, we can use the searching for the Factor VIII (F8) gene as an example of interacting with the SVA genome browser.

Type in "F8" in the "gene symbol navigating" drop-down box, then click on ">Search gene" button at the right. It may take 30 seconds also for SVA to collect the data in this region. You will first see a note like this:

This indicates that SVA has found that the F8 gene on chromosome X, with three annotated transcripts (only one of them will be the most common, or 'canonical' transcript, which will be described later in this page). This note also gives the Ensembl stable ID and the coordinates for these three transcripts.

Then you will see that the SVA genome browser displays an image including several sections, described in the next page >>>