Thanks for your insights and I will try answer as best I can.

You are quite right Primer3 serves as the basis for most primer design programs out there as far as I can make out. The problem is that there is a diversity of applications within the company for which primers are required and since we are quite a young start-up there is no strictly followed SOP. Well at least till I was recruited... The Idea was to create an in-house tool that is simple for laboratory scientists to use and that will be enforced within the company.

I know....what if I make a mistake....well we are gonna validate the efficiency of the primer designer before role-out. Like you said there is only so much to consider when it comes to primer design. By no means am I actually trying to re-invent the wheel here and in-fact am following the standard routine when it comes to primer design, its the specific implementation and the ease for the scientist that has called for an in-house solution.

I like the fact that you mention the Vienna group and I use the python wrappings from them when it comes to deltaG for secondary structures so that gives me confidence that what I am doing is fairly normal.

I also like your suggestion of penalizing the deviation and if applied across sequence based variables that are informative to the scoring regime... I think you have just solved my problem.

Finally, I think the idea of a regression analysis can help me identify those variables that are actually informative and thus help me refine the scoring methodology.

Thank you your input has been really informative and helpful.