Tutorial Instructions

At the right you will see a compact version of the viewer. Follow along with the tutorial instructions at the left, while you perform them at the right.

You may wish to expand your browser's window at this point to make viewing easier.


1. Pick Chromosome Pair

Choose the pair of chromosomes that you want to look at. Do this by clicking at the appropriate row and column in the table at the bottom of the page. Each combination of chromosomes appears twice in the table, once for each possible orientation.

This will bring you to the viewer screen and will display the entire matrix of your chosen chromosomes.

2. Zooming In

Click on the image where you want to zoom in. The feature you clicked on is now approximately twice as big as before. This is because the zoom magnification is initially set to twice (2x) and you haven't changed it yet.

Try zooming in again - the image will get twice as big again, a total of four times larger than originally. This cumulative magnification is shown below the image.

Notice the graphic under "Region Displayed" at the left. The small gray square within the larger black box shows you the extent of your current view within the context of the entire matrix. Keep an eye on this as you continue.

3. Zooming Out

Change the zoom direction to "Out" by pressing the "out" button under "Zoom Direction."

After the screen redraws, click on the image where you want to zoom out.

4. Change Zoom Magnification

Until now, when you zoomed in or out, the magnification changed by a factor of 2. This is the default when you begin. Perhaps you would like to zoom in faster.

To do this, press the button for one of the higher zoom speeds (5x, 10x, 20x) under "Zoom Magnification." Also change the zoom direction back to "in." After the screen redraws, click on the image where you want to zoom in.

Feature Bars

As you zoom further in, eventually colored bars will appear along the axes, indicating where genetic features are located on each chromosome. Blue bars indicate Watson features and green bars indicate Crick features. If you continue to zoom in, labels will appear identifying the features.

5. Going to Gene/Sequence Resources page

A small form beneath the image allows you to go to the Gene/Sequence Resources page with the visible sequence of either chromosome or with any visible feature if zoomed in far enough for feature labels to appear.

Try this with a sequence by pressing the radio button for either sequence and then pressing "Go to Gene/Sequence Resources." This will bring up the Gene/Sequence Resources page which gives many options for displaying your selected sequence.

Help for Gene/Sequence Resources

5. Scrolling

Suppose at this point you'd like to see what lies just off the screen in some particular direction.

Under "Scroll," at the left, press the button that corresponds to that direction. The view will "scroll" one-half screen in the direction that you chose.

6. Zoom Completely Out

Press "Zoom Completely Out" at the top of the page. This will bring the full matrix back into view, just like when you started.

7. Change Minimum Size

The current view only shows similarities larger than 30 base pairs in length. Although the data set contains similarities as small as 20 base pairs in length, the default is set higher to help reduce the "noise." Try decreasing it to 20 by pressing the corresponding button under "Minimum Similarity Size." The view will redraw itself with the new size cutoff.

8. Change Image Size

Depending on your screen, the images might not have fit well in the area where they're displayed. The size is currently set to 300 pixels. You can change that by pressing a button for a different size under "Image Size." Try reducing the size by pressing 250. The screen will redraw itself at the new size.

9. Perform Custom Re-Scan

When you zoom very far in (i.e. when a side spans less than 2500 base pairs), you have the option of performing a custom re-scan. This link appears at the top right when you have zoomed in sufficiently far. The purpose of a re-scan is to more carefully search the current view area. A detailed description of this feature's capabilities is presented upon choosing the link.

10. Pick Different Chromosomes

Congratulations! You have now used all the features of "Pairwise Chromosome DNA Similarity View." The only thing left to do is to choose a different set of chromosomes to work with. To do this, press "Pick Different Chromosomes" at the top. This will bring you back out to the introductory screen where you can choose a new set of chromosomes from the table at the bottom the way you did before.

For additional information about the settings or how the data were initially generated, select "HELP" in the upper right.

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