You can use the DNA Matrix Analysis display dialog box to filter results and display the following:
- matrix map
- aligned sequences.
1. The DNA Matrix Analysis dialog box is displayed on completion of each analysis. To display this dialog box at other times, for example to change the display parameters, choose Analyze | Pustell DNA Matrix when any matrix analysis display result window is active.
2. You can limit the display to a region of each of the sequences by typing in the numbers that bracket the region in the X-axis and Y-axis text boxes, or by selecting a region from the features table drop-down menu that appears to the right of the text boxes.
3. If you chose both for the analysis strand setting, you can now choose to display the comparison of the plus strands only (++), the plus strand of the X-axis sequence with the reverse complement strand of the Y-axis sequence (+-), or both. If you limited the initial analysis, you will not be able to display the other types of comparisons.
4. If you set jump to both in the analysis, you can now separately display the matches found for the jump setting of 1 and the jump setting of 3, or you can look at both simultaneously. If you limited the initial analysis, the drop-down menu for the jump setting will be disabled.
5. Enter a value for the window size in the window size text box.
This can have any value starting from the window size used in the original analysis stage up to 60.
6. Enter a value for the score in the min. % score text box.
This can have any value starting from the min. % score used in the original analysis stage up to 100.
7. Select the matrix map check box to display a dot matrix plot of the results of the comparison.
8. Use the drop-down menu at the end of the Matrix map check box to choose how you want to display the matching regions.
The line setting displays matching regions as diagonal lines. The character setting displays matching regions as diagonally arranged characters. The character used indicates the percent match at that point along the diagonal. "A" represents 100 percent match, and each succeeding letter is two percent less, so "B" is 98 percent, "C" is 96 percent, and so on.".
9. Select the Aligned sequences check box to see a display of the X-axis sequence aligned with all of the regions of the Y-axis sequence that meet or exceed the min. % score.
10. Select OK to display the results.