# 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.

## Quickstart

• 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.