Figure 2. The genome browser window.

The window is divided into three panes: (A), (B), (C). (A) shows the map of the annotated features, (B)—nucleotide/amino acid sequence of the currently highlighted part of the feature map, and the bottom one—the results of database searches. (C) is a tabbed web browser with navigation commands available via contextual menus. This allows to investigate the details of a particular search hit quickly. Hovering the mouse pointer over a feature in the top pane pops up a small window displaying its current annotation (shown). Clicking on a feature selects it, right-clicking displays a contextual menu allowing to launch a number of web-based searches with a selected feature as a query; the menu also has commands for feature copying and editing. The toolbar on top of the window contains a navigator control (on the left) allowing to scroll the sequence display from one hit to another. The information on the currently selected hit is shown to the right of the navigator. The search field distinguishes three query types automatically: nucleotide sequence, coordinate and annotation text. The rightmost control allows to zoom the feature map in or out. This example shows the browser window in the middle of analysis of a search with Fur binding site profile. The currently selected (and highlighted in the top and middle panes) Fur binding site is located in front of a large operon on the bottom strand, most of the frames in which were originally annotated as “hypothetical protein.” Searching the Uniprot and especially the Conserved Domain Database (the actual result of CDD search with one protein coded by this operon is shown) revealed that all these frames code for components of the type VI secretion system, which is known to be controlled by Fur.