Individual sequences can be colored and each sequence is interlaced with the others to allow easy comparison. Any number of individual sequences may be placed into a singe sequence document. An overview "pane" at the top of this window shows which segment(s) is being displayed in the sequence pane and can be used to navigate to specific locations in specific sequences.

The sequence editor also is the tool for displaying multiple sequence alignments as shown in Figure 3.

This alignment window shows a histogram scoring row at the top (red), a consensus sequence next (blue), and then the aligned sequences themselves (black) with shading intensities indicating the extent of matching to the consensus at each position in the sequence.

Define Analyses Using Analysis Setups
The Gene Inspector provides a means to run analyses in a very intuitive manner. Analyses are first chosen from a scrollable list. As an item in the list is selected, "help" information appears next to the selected analysis describing that analysis. Once an analysis is chosen, an Analysis Setup Panel is presented as seen in Figure 4.

The icons on the left of this panel represent different aspects to the analyses to be performed. The "hydropathy" analysis icon is selected on the left and the rest of the window on the right shows information about and parameters for that specific analysis. Other icons in this Analysis Setup represent a "find repeats" analysis, an input icon to define which sequences are to be analyzed, and an output location icon, to define the notebook into which the results of the analysis will be placed. You can add as many analyses to an Analysis Setup as you choose to run. Once you have defined an Analysis Setup that you would like to use in the future on different sequences, you can add the it to the Analysis menu. To recall it, just select it by name from the menu. This means that anyone in your lab group, whether an expert or a novice, will be able to perform the same analyses with the same parameters and therefore get results that are consistent.

Illustrating Sequence Features
The Gene Inspector also allows you to display in the notebook an annotated sequence as a "features" object, shown in Figure 5.

Restriction sites can be marked, translations performed, introns can be defined, and font size, style, and sequence grouping can be specified. You can choose to use any font to display any part of a sequence and are not restricted just to monospaced fonts. Special styles like "box around" provide you with the tools to display your sequence with all important features illustrated in precisely the way you want to display it. This is perfect for making publication figures!