Hello, I designed some primers using the http://www.premierbiosoft.com/isothermal/lamp.html. The software is very easy to use but is expensive...I used the free trial for few days, not all my primers were working so before buying it I want to try the https://primerexplorer.jp/elamp4.0.0/...
I have a question concerning it...I MADE my parameter more strict, but I still have more than 50 sets.. when i used the old software it only gave me 10 set at max and it was easier to check them on blast and the secondary structure...How do you select the best one from your list, besides checking the dG?is just random ?
Thanks
For which use are you designing the primers? i always use a free program called Primer-Blast on the NCBI website to design qPCR primers: http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome
Primers for cloning is develop myself by looking up the sequence, choosing a location for my primers (you could use Ape for this), and blast them in NCBI.
Hi Anouk, thanks for the answer.
I did use Blast for RTPCR too and use the web to double check my primers afterwards. it works fine. In this case I need to develop a LAMP ASSAY for diagnosis in plant pathology so I need the 4 primers and will be a pain to design them looking up on the sequence, expecially if I have more than 1 target...
Hi Rosa,
You could try Beacon design, but it is unfortunately not a free program.
Hi Rosa,
I use VisualOMP software to test my primers before ordering them. It is very easy to use and you can run in silico tests to see if your primers are good or not. However, you won't have a final result until you don't test them at the lab and see if your NTC is clean and you get good positive amplification and high sensitivity.
Good luck
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