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tool for comparing many primers pairs

primers cross reactivity

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4 replies to this topic

#1 Ann.op

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Posted 17 February 2014 - 04:01 AM

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

 

 

 



#2 hobglobin

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Posted 17 February 2014 - 09:37 AM

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


One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

That is....if she posts at all.


#3 Ann.op

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Posted 18 February 2014 - 10:39 PM

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



#4 neuron

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Posted 19 February 2014 - 04:25 AM

Here is one more link-

 

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



#5 hobglobin

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Posted 19 February 2014 - 09:14 AM

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.


One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

That is....if she posts at all.






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