Hello, I want to ask you about probelms of primer3 program.

[Soyulsoyul]

Hi, I'm Soyul Ahn, graduate student studying in Pusan University, Korea.
Recently, I have an issue about primer3 program.
Several weeks ago, I leave a message to '[email protected]' to ask about the issue, and they replied report the problem at this page.
Here's the problem. My colleague and I used primer3 to find TNF-a primer with size limitation 100-200. I used ver.4.0.1, and my colleague used ver.0.4.0. The result was different. I attached the result page. I'm curious why this issue has happened.
I'm looking forward to receiving your reply.
The above is version 4.1.0 and the below is 0.4.0.

[untergasser]

Hi,

you are asking why an 20 year old car drives differently than a modern one? Lots of things changed between the versions and things got optimized. Look at GitHub for details. I think you can still get the same result like version 0.4.0 if you use the right parameters, but it will not be the best primers you can get...

I hope this helps.

Best,

Andreas

[Soyulsoyul]

Thanks for your comment.
There's something missing from what i asked before.
The result of qPCR experiment didn't come out properly with the primer made with version 4.1.0, so I made the primer again with version 0.4.0. And it worked well.
All other experimental conditions were same, obviously.
I don't know much about programming, but I think the new version should be upgraded compared to the old version.
Now I'm asking you how to solve this problem because the result that didn't come out in the ver. 4.1.0, came out with the primer made with ver. 0.4.0.

[untergasser]

You picked one primer on a complete different location which worked in your hands better. This could be different with the next set of primers - and even improved if you enter the right PCR conditions in Primer3. "result that didn't come out" is also not describing well what you did and what came out, so my advice at this point would be to read the manual of Primer3.

Best,
Andreas