What is your favorite tool for primer design ? - (Sep/27/2007 )
There are many tools on the internet. But, I don't know what is the best.
Tm of a primer [5'-CCA AGC GAA TCT CTG TAG'3'] derived from [http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx] and [http://www.basic.northwestern.edu/biotools/oligocalc.html#helpthermo] are quite different.
I don't know which one is more reliable.
Please, share your experience of primer design by using your favorite tools.
Which one is the best in our opinion ?
Primer3,The best and simplest tool for DESIGNING primers.
For oligo analysis idtdna is good.
primer3 is a great tool. I have used it in the past.
now i have bought a program. also you need an oligo analyzer.
what i do:
I design primers in primer3 lets say, then i check them in an oligo analysis program, and then i blastn them.
Thats the 3 keys for me.
However there is always diferences in Tms from primers, even the Tms that the company who makes the primers send you!
So my opinion is that you got to find a program and to stik to that. keep it and always work only with that.
For instance I know now that a primer that i design and the program says Tm 66 I really work the primer at 58.
So in my opinion you have to standarize your procedure...
hope to helped