The Sequence Window IV
This second example shows how an analysis can be made at the DNA sequence level. To create this example, we started by displaying the DNA sequence and DNA_Analysis window as described in the previous page. (Select DNA sequence, and unselect "3 Frame Translation" and ORF's in the Columns menu. Then select Analysis window" in the Sequence window popup menu.) Once the DNA_Analysis window is displayed, click on the "Show gels" button with the leftmost mouse button. This brings up the Agarose Gel window. In the yellow data input box, type in a sequence motif, in is this case we used BccI, and pressed the return key. (We could also have typed the recognition site itself, CCATC; if the name of a restriction enzyme is entered it must match the name of a member of the Motif class).
A representation of an agarose gel is produced. (You may need to resize the window to get a good view.) The blue horizontal bars represent the bands that would appear in the gel, if the sequence were cut at positions containing the given motif. Band sizes are displayed by clicking on the "Coordinates" button. Also notice that the positions of the motif are highlighted in light blue on the DNA sequence and on the vertical yellow sequence bar at the left in the Sequence window.
We have double-clicked on one of the bands in the simulated gel to illustrate another feature. The region of sequence associated with the band is now highlighted in dark blue in the sequence window - both on the vertical yellow bar and in the sequence listing itself.
Although it is not shown in this figure, it is possible to look for restriction enzyme sites in the sequence using only the DNA_Analysis Window. Simply type in an enzyme name in the yellow text entry box and press return. Once again the motif is highlighted in the DNA sequence, and the positions of the sites through out the sequence are shown by horizontal lines on the yellow sequence bar.