The Rat GBrowse Genome Browser
The GBrowse Search Box
|
|
|
To select a region of the genome to view:
- Enter its name in the text field labeled “Landmark or Region”. Recognized types of names/symbols are genes, QTLs, markers, strains, database accession numbers, disease terms, or chromosome number with coordinates.
- Click the “Search” button.
|
Navigation Functions
|
|
|
Once a region is displayed, you can navigate through it in a number of ways:
- Click and drag on a ruler in the “Overview”, “Region” and “Details” panels. Click once to recenter the view at the desired position, or click and drag to select a region.
- Scroll left or right with the <<, <, > and >> buttons which appear in the “Scroll/Zoom” section of the screen, and at the top right and left corners of the “Details” panel. The << and >> buttons scroll an entire screen’s worth, while < and >> scroll a half screen.
|
3. Zoom in or out using the sizing selection drop-down menu (“Show # bp”). The menu item name indicates the number of base pairs to show in the full width of the “Details” panel. For example, selecting the item “100 Kbp” will zoom the “Details” panel so as to show a region 100 Kbp wide.
4. Make fine adjustments (10-20%) of the zoom level by clicking the “-” and “+” buttons adjacent to the sizing selection drop-down menu.
5. To flip the browser display so that the sequence coordinates increase from right to left in the “Details” panel, select the “flip” checkbox. |
|
|
[Return to top of page]
Selecting/Deselecting Tracks
|
|
|
To expand/restrict the scope of the displayed information, click on the “Select Tracks” link from the menu bar on the upper left side of the page (1), or either of the two “Select Tracks” buttons found near the bottom of the page (2) to return the “Select Tracks” tab. |
|
|
|
|
|
|
|
The “Select Tracks” tab features a track search text box and an expandable list of data tracks which can be selected/deselected by the use of checkboxes. To view selected tracks click on the “Back to Browser” link at the upper left of the “Select Tracks” tab (1) or on the “Back to Browser” button at the bottom center of the page (2). |
[Return to top of page]
Upload, Downloads, & Preferences
Additional functionality of GBrowse is found in the tabs/menu bar at the upper left part of the page and in the drop-down menu above the zoom drop-down menu. |
|
|
- Upload and Share Tracks: Clicking on this link/tab reveals options to upload custom tracks from text, URL, or file. Detailed help describing the upload process is available here and from that tab.
- Preferences: The preferences tab allows the user to customize the GBrowse interface to personalize the look of the display. Display width, gridlines, and highlighting are among the changeable properties.
- Downloads, etc: The drop-down menu above the zoom drop-down menu has options of sequence downloads, track data downloads, and data filtering. Clicking the “Configure…” button to the right of the drop-down displays the selectable parameters for the particular choice made in the menu.
|
[Return to top of page]
|
|