Finding MLPA probes

This assignment was about finding MLPA probes. I had to make a couple of changes to an existing program to implement this. See this paper for the complete description of the assignment.


  • Get release 0.9 of Primer3.
  • Get this patch.
  • Patch the source code by doing:

     cd primer3_0_9_test
     patch -p1 < ../primer3_0_9_test_p/primer3_0_9_test_p.patch
  • Recompile the code.

Primer3 will now recognize two more input tags:

  • PRIMER_CONTACT (Default =0, set to =1 to find two primers with no space between them).
  • PRIMER_SAME_STRAND (Default =0, set to =1 to find primers on the same strand).

The patch archive also contains a patch for this perl script. This script iteratively calls the Primer3 executable.

Look here for more information on Primer3.