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tool for comparing many primers pairs - (Feb/17/2014 )

Hi

 

I have some pairs of primers, each of them works very good. 

I'm looking for a tool (in situ) which can compare them all togather to find cross reactivity. 

(NCBI or UCSC for example, know to compare only 2 primers)

 

does anybody know about a software/ website that can help me? 

 

thanks,

Ann

 

 

 

-Ann.op-

have a look here, I guess you find what you need

-hobglobin-

have a look here, I guess you find what you need

 

Hi again

 

I just try to understand how does it work

 

after inserting my primers, I got scores- where can I find the meaninig of it? 

 

How can I know which score says that I can't use the pimers together? 

 

BR

Ann

-Ann.op-

Here is one more link-

 

http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/

-neuron-

okay you want to use them as multiplex primers...what you can do is to compare Tms (they have to be in a similar range) and test one against each other in pairs to see if they form secondary structures. One tool would be Multiplx: http://bioinfo.ebc.ee/multiplx/ (online or standalone) which is doing this for you to some part and which is quite self-explanatory.

Anyway as far as I know to be really sure if it works is trying out in the lab, as all analysing and scores stuff are just estimations based on the parameters used by programs. Even if a program tells you that primers fit perfectl, it might not work in the PCR tube and vice versa.

-hobglobin-