Hey, im trying to design primer for my genes which im going to study on... im using "PerPrimer", "Primer3", "Primer BLAST" and " IDT" softwares for designing and cheking as if it forms hairpin, primer dimer &....
I've come across with so many different results which makes me confused, the primer that is designed by Per Primer is not acceptable by Primer 3 and vs.
could you please help me !!!!! can you suggest me the best way to continue on?????
Hi, primer3 is the best software for primer design.
http://simgene.com/Primer3
Best regards
Dear Samira
I do not know PerPrimer but I know Primer3 and I consider it a well developed software. I have done good experiences with it.
Be aware that "Primer BLAST" in the NCBI website uses Primer3 as well. The difference is that -additionally to the primer design- it makes a BLAST search of proposed primers. This way you will know how specific are your primer sequences, if they do bind with other organisms or if they bind with several loci whithin the same target genome (what is problematic).
I recommend you to work with Primer3.
Greetings!
carolina
Hi,
I am agree with the previous answers. I use Primer3Plus to design primers, I choose the best according to the criteria I need and I also control parameters ANY, SELF...Then I check them using "PCR Primer Stats" (http://www.bioinformatics.org/sms2/pcr_primer_stats.html). I have good results.
Best regards.
Hi,
I do agree with all above answer. I used primer3 for designing different primers and all worked well in PCR reactions.
Hello Samira,
I would also suggest Primer 3. The program is complex enough for primer design.
But, in general, keep it simple, cause simple things work.
Best regards
Dirk
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