Introduction

The Java GBrowse is a Java Applet-based implementation of the original CGI-based GMOD GBrowse web application developed by GMOD. Although similar to the CGI-based GBrowse application, Java GBrowse has some new functionality, including more search options, and a modified navigation interface. With a few exceptions, Java GBrowse can be used with the same configuration and database as the original CGI-based GBrowse. We currently only support a subset of the configuration options offered in the original GBrowse, we hope that we have captured a rich enough sub-set of the functionality to meet the needs of many configurations.

The Java GBrowse can display many types of information about a genome that are specific to its configuration--some possibilities include genes, ESTs, or contigs. This data is arranged into separate tracks and is aligned to a reference sequence that is specific to what is being viewed (e.g. chromosomes, contigs, etc.). The reference sequence determines the base pair axis for the data.

Views

There are two main views of the data in Java GBrowse--the overview and detail view. At the top of each of these views is a ruler that relates the data in the view to its corresponding base pair position (in relation to the reference sequence). The overview shows a "bird's-eye view" of the entire base pair axis for the reference sequence. Within the overview is a red rectangle that delineates the base pair region of the overview that is being expanded in the detail view (note, the rectangle in the bird's eye is referred to as the cross-section).

Navigation

Clicking in the overview will move the region that is displayed in the detail view so that it is centered around the mouse pointer. Several additional navigation options can be accessed through the toolbar above the overview.

Reference Sequence Drop Down

The selection in this drop down menu determines what reference sequence (chromosome, contig, etc.) is being displayed in the overview and detail view.

Choose Track Drop Down

The selection made in this drop down impacts searching and the action of the Next Entity in Track Button.

Next Entity Button

Pressing the button will cause the detail view to center around the next entity in the selected track and will highlight it. (The track selection is made using the Track Drop Down.)

Full Left/Right Buttons

These buttons move the cross-section that is displayed in the detail view to the left or right by full width of the view.

Half Left/Right Buttons

These buttons moves the cross-section that is displayed in the detail to the left or right by half of the width of the view.

Zoom In/Out Buttons

These buttons decrease (zoom out or "-") or increase (zoom in or "+") the resolution of what is being view in the detail view. (This is done by increasing or decreasing the width of the detail view cross section by one tenth.)

Zoom Drop Down

The selection in this drop down gives the width of the detail view cross-section in base pairs.

Customizing the Detail View

Horizontal Ratio

This drop down can be used to magnify the data in the detail view without changing the width of the cross section being viewed.

Vertical Limit

This drop down can be used to limit how large the detail view can expand vertically in terms of the height of the screen. If the threshold is reached, a scroll bar is added.

Searching

To search for a named entity, type its name into the box and press the Go Button. The wildcard character ("*") will match to any combination of 0 or more characters. If the results of the search are ambiguous, a dialog will be displayed listing all matching entities, and the desired entity can be selected. The results of the search can be filtered using the two check boxes options to the left of the Go Button.

This <Reference Sequence> only

If this is checked, the search will only be made within the current selection in the Reference Sequence Drop Down.

Choosen Track only

If this is checked, searching will only be done within the track currently selected in the Choose Track Drop Down.

Changing Track Options

Tracks can be show or hidden by setting or clearing the check box for the track below the detail view. The changes do not take effect until the Update Tracks Button is pressed. To configure more options for the tracks, press the Set Options button to open the Track Options Dialog.

Show Checkboxes

Clear to make the corresponding track hidden.

Format Drop Downs

Used to determine how collisions of multiple overlapping entities are handled.

Compact: allow overlap--all entities in the track will be drawn in a single row.

Expand: entities will be moved to new rows as necessary to prevent overlap, but labels will be omitted to save space.

Expand and label: same as expand, but all named entities will be labeled.

Auto: automatically chooses between compact and expand and label based on the density of the data in the track.

Re-order Drop Downs

Use these to move the selected track to the row containing the drop down.

Undo Button

This button resets all options to their state when the window was opened.

Revert to Default Button

This button resets all options to their defaults (as specified by the Java GBrowse configuration).

Cancel Button

This button closes the window and discards any changes.

Accept Button

This button saves all changes, closes the window, and redraws the detail view according to the new settings.