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primer-blast from ncbi


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#1 wntiong

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Posted 24 November 2009 - 05:25 PM

Has anyone use this software before?

I am new in pcr primer design and want to design primers for rt-pcr. This software has involve chossing of exon-exon junction for users so i thinking to use it. But, how does it compared with primer3? which is better?

thanks

#2 Rsm

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Posted 24 November 2009 - 05:57 PM

Has anyone use this software before?

I am new in pcr primer design and want to design primers for rt-pcr. This software has involve chossing of exon-exon junction for users so i thinking to use it. But, how does it compared with primer3? which is better?

thanks


I think primer-blast is the best site around these days. It implements the original Primer3 algorithm. However, one difference is the annealing temperature calculation, while Primer3 was always a bit too high (you'd have to input 62C to get a primer for 60C), Primer-Blast is correct. Recommended!

Cheers,
Minna
I got soul, but I'm not a soldier

#3 DigitalPig

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Posted 24 November 2009 - 10:06 PM

Has anyone use this software before?

I am new in pcr primer design and want to design primers for rt-pcr. This software has involve chossing of exon-exon junction for users so i thinking to use it. But, how does it compared with primer3? which is better?

thanks


For me, I used PerlPrimer software to design the primer for real-time. You can google it to find the download link.

#4 wntiong

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Posted 25 November 2009 - 12:47 AM

Thanks guys,

i used both primer3 and primer-blast to design primer for same gene, then blast both forward and reverse primer sequences. Apparently two different set of primers were produced and after blast, the primer3's primers showed e value of 0.0015 to that gene's genomic sequence and about e value = 248 for the next genes. for primer-blast's primers showed same e value of 0.0015, but if against to next other gene, it is about 3.5 of e value.

i am not sure. but since the primer-blast has the option to find the exon-exon boundary, which is better according to above blast results?

i am really a beginner onto this, kindly advise though if the question sounds stupid. lol.

thanks




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