Hi Mehrdad,

Using the geneious software program for example, the primers are going to be named as the first base position of the fwd primer from the 5' end and the last base position of the rev primer on the 3' end. So this would be A and D in your example.

I'd suggest you start by reading about PCR in a textbook or watching some training videos. Cold Spring Harbor lab has a great one.

The way you've asked your question tells me that you need to learn more about the basics.

Good luck!

Hi Mehrdad,

Using the geneious software program for example, the primers are going to be named as the first base position of the fwd primer from the 5' end and the last base position of the rev primer on the 3' end. So this would be A and D in your example.

Hi Mehrdad,

PCR primers are included in the PCR amplicon. But I agree with Katie, maybe it could be a good start for you to read more about PCR and understand the method before use it. Otherwise, you will not improve your skills.

Good luck

Eric Gismondi

I think you and Katie misunderstood my question. It is related to the 926 and 1392 primers' bases/ nucleotides positions. I am looking for the four probable positions of the bases. It has nothing to do with PCR principles, I suppose. Joshua Philips answered my question! Thanks, dear friends.

Hi Joshua Philips

Thanks a lot, sir. I checked out the software. Sadly it is not free. Have you checked out the primer set F-926/R-1392 positions? Is it shown the positions on that software, i.e. the first base of 5 prime (926) and the last base of 3 prime (1392)?

Can you introduce me free software if you know?

Yes Mehrdad, Joshua answered the same as me when I said that the primers are included in your amplicon . Anyway... you have your answer, that's the main thing ;)

Eric Gismondi

Thanks, man. Anyway, I wanted to know the exact position of the base number 926 in primer from the forward side, for example. Is the base located in the 5'-end of the forward primer or 3'-end of the forward primer! That was the point.

Best regards,

Mehrdad Rabiei You can have Genious free trial for two weeks.

Ah, sorry for misunderstanding your question. Joshua is correct, but this does assume the person who named to primers followed that convention.

You can also just BLAST the primers to be certain.

Katie A Burnette

It is OK! Thanks for caring and replying. You are right! BLAST would be helpful, but primer pair like this one cannot be blasted because it has degenerate nucleotides. As you know, BLAST does not accept ambiguous nucleotides, such as M, D, ... . It makes it difficult. :)

Best regards,

Hi,

I agree with Joshua Philips , It should be A and D, that is, if the person who designed them followed the "general logic of primer design" (And that, personal experience, would be my source...). It is definitely the best educated guess. If that person used some personal logic, it may be that the reverse primer is named after C, but I find it rather unlikely (if they had any previous personal experience in primer design, that is).

Hope that helps

Thomas Mühlenberg

Thanks, sir. You know what? There are two terms: 1-PCR product (targeted region, primer pair and ...), and 2-PCR amplicon (interested region without primer).

In microbial reads analysis, researchers need PCR amplicon (targeted region) to analyse their data!

When I see the nucleotides number positions of primer set, I do not know exactly where is the actual their position; I mean are the digits revealed after or before trimming of primers or not!? In other words, are the numbers related to both ends of a PCR amplicon (only targeted region) or PCR product (Targeted region plus primer)? I tried to give this explanation to make it easier and show what is behind the question I asked.

Anyway, thanks for your reply.