Any primer design programs...? - (Sep/18/2006 )
I recently "eyed" some primers for my research but am only getting one band in the targeted region when I run my gel. Is there any program that would help me design my primers and hopefully choose "better" ones? I am a new grad student and trying to learn my way around the lab!
I use Primer Express. It's an Applied Biosystems program and seems to work fairly well.
There are number of free programs to try. Primer Express from applied biosystems is not availabale free of charge. There are also some programs you pay for. The more you are designing primers, you will become better at eyeballing them. The most important factor is calculating the Tm. I use the IDT ologo analyzer for that, but other coompanies use different algorithms that can produce varying results.
As mentioned before, there are a number of free primer design programs on the Web.
I personally use Primer 3. It has not failed me so far.
My favourite programme is NetPrimer, available for use on the Internet: http://www.premierbiosoft.com/netprimer/ne...etprlaunch.html (they used to let you download it, but now you have to use it on-line, but it's free). It won't find primers for you, but it will nicely analyse primers, or pairs of primers - Tm, hairpins, dimers, etc.
There is a pinned thread here: http://www.protocol-online.org/forums/index.php?showtopic=13
As I remember right "Primer3" was the favorite of most users. I use Oligo 1.0, an old DOS version someone donated to me.
free primer design programs can be accessed from the net where you need to give only the Genbank nos or copy paste the sequences with ur essential parameters..i hav tried 'FastPCR' which is a free primer design software..
pls try downloading it and see if it turns out to be useful..
I have used Primer 3 (linked to above by perneseblue) for thousands of primers -- it has my recommendation...
Thanks for the help!