I was hoping that someone might know of a good probe design software. My method is sort of based off of the oligo ligation assay and MLPA but it's not exactly either of those. I just want to be able to have something that if I input a sequence with a SNP, it will return the upstream hybridization oligo and downstream hybridization oligo to a SNP site. I have attached a photo to describe what I mean. I realize this might not be the best forum to post this in, but I don't know where else to ask. My goal would be to make hybridization oligos within a specific size range, close Tm, and 50/50ish GC content. I can do this by hand for a couple but I would like to expand my project to a couple of hundred sites. If anyone has any program suggestions I would appreciate it. Ideally something a dummy (like me) could use or at least a program with some tutorials. I have looked into Probemaker but even that seems awfully complicated. Even if the program isn't free I would look into it.
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