I'm trying to design primers which contain deoxyinosines, but I was wondering if there is any specific software or a well known software which help me calculate the °Tm and other thermodynamic parameters for a primer with deoxyinosines??
I used oligocal form northwestern for a similar purpose (modified bases). on top left corner a link is present which re-directs you to codes for nucleotides (I- ionosine in your case). It also gives detailed information for its calculation parameters. What I like most is the fact that it gives you the basic, salt adjusted and nearest neighbor Tm (last one in my experience has been the most accurate for my applications). Hope it helps :)
Thanks for your suggestion Rachayata, but how do you use it to analyze a degenerate primer? I was trying, but I couldn't do it. And Rayne, yes Primer3 gives you the parameters; however, it doesn't accept other letters in the sequence than A,C,G,T; so, for this purpose (analyzing a degenerate primer) Primer3 doesn´t work.