This output combines the TestCode result along with an indication of open reading frames (ORFs) and rare codon usage. Taken together, these three analysis results point to the indicated ORF as being a true coding region. As a biologist, you might next want to translate that ORF and examine the peptide. This is easily done by clicking on the ORF arrow with the mouse and translating it directly to a peptide sequence using the "translate" menu option.

Another example of an interactive analysis is the dot matrix analysis as shown in Figure 7.

In this output, different colors represent different extents of similarity between the two sequences (in this case red is the most similar and blue the least similar regions above the threshold). To see what the actual sequence alignment looks like for any particular region of the plot, just select the region with the mouse and choose "align selection" from a menu. This will produce Figure 8, an alignment of the two sequence segments selected in the dot plot.

For this particular instance, a region of interest in the graphical dot matrix plot, was examined further by directly creating the sequence alignment output. There was no need to go back and start the analysis all over again. This free flow of thought allows you to concentrate on the meaning of the results rather than on how to run the program. This kind of interaction occurs throughout the Gene Inspector to provide you with a comfortable environment in which to store your experimental results and sequence analyses.