The next two examples show a few of the tools that are available to analyze protein and DNA sequences. To reproduce the example here, first click the Columns button and select "3 Frame Translation" and ORF's, as described in the previous example. The window will be filled with the translation of the chalcone synthase sequence in all three reading frames (5' to 3'). Stop codons are indicated by asterisks and by the horizontal lines to the left of each translation. Notice that there are no stop codons in the regions where the protein homologies are shown (filled blue rectangles).
The dot "." that follows each row of the amino acid translation indicates that the full sequence in not shown on the window. The amount of translated sequence which is displayed is a function of the "DNA width". You may set the DNA width only after you display the DNA sequence (via the Columns button). Once the DNA is displayed a new button appears, "Set DNA width". Click on that button and fill in the blank on the new pop up window to either increase or decrease the width.
In order to bring up the DNA_Analysis window as shown in the figure, open the Sequence Window pop up menu by pressing the rightmost mouse button, drag down to the bottom to the "Analysis window" option, and release the button. The next example shows how ACeDB can be used to simulate restriction digests and locate restriction enzyme recognition sites.