CSC334 Lab4

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Finding repeats in DNA sequences

In this lab you will work with a Proce55ing sketchbook to create a graphical representation of repeating sequences in DNA sequences. Finding repeating patterns, either adjacent to each other, as in tandom repeats, or long interspersed repeats yield important genetic information about a DNA sequence.

Repeats can also be found comparing the sequence to its reverse. Biologists are interested in repeats because they are often indicative of genome rearrangements.

Methodology

• Copy and paste the program DNA_Repeats_start.pde in a new sketchbook which you should call DNA_Repeats.pde.
• Create the font needed for the program. Click on Tools, Create Font, and select Monaco, with a size of 12 points.

This will create the file Monaco-12.vlw in the data folder of your Processing sketchbook. If you cannot find the font Monaco on your computer, select a monospace font such as Prestige Elite, or Courier.

• Run the program. Verify that you get a empty square and a listing of the DNA sequence

Step 1: Finding repeats

This part involves the whole class to discover the algorithm that can be used to find repeat patterns longer than some predefined length.

• come up with an algorithm (this will take some time!)
• code it, and test it. Use a minimum length of 1 or 2 at first, and increase it slowly to see the longest pattern founds.
• verify that you get an image similar to the one above.

Step 2: finding the longest repeat

• Make your program print in the console the locations of the longest repeats it finds, in the following form:

 longest repeat:  123,  255  length 7  CGGTAAC

This means that a sequence of length 7 was found at Index 123 and at Index 255, and reads CGGTAAC

Step 3: Marking the longest repeat

• Once your program works, make it display a circle around the longest repeat (or repeats) found. Use the drawPoints( int i, int j, int n ) function as an example for a new function putCircleAround( int i, int j, int radius ) that could be used to highlight the longest segment.

Note that to draw a circle that is not filled with color, you use the noFill() function and call ellipse().

  noFill();
  ellipse( x, y, radius, radius );

Solution Program

• DNA_Repeats.pde

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© D. Thiebaut 2008