I'm not familar with IDT's "OligoAnalyzer Tool". I didn't even know offhand that it uses UNAFold.
Assuming they are, I don't know precisely which version of UNAFold they use. It could very well not be UNAFold 4, which I assume is what you have, although I wouldn't expect any differences that are all that significant. It could also be that they used different options than you did. If IDT showed you multiple structures, I imagine they obtained them with the --mfold option; did you use that as well? If you didn't request suboptimal tracebacks in the first place, that could be an obvious and fairly uninteresting explanation.![:D]( "Very Happy")
If you're interested in replicating their results exactly, I suppose your best bet is to contact IDT and ask them exactly what version of UNAFold and what options they use.
Hope this helps!
Assuming they are, I don't know precisely which version of UNAFold they use. It could very well not be UNAFold 4, which I assume is what you have, although I wouldn't expect any differences that are all that significant. It could also be that they used different options than you did. If IDT showed you multiple structures, I imagine they obtained them with the --mfold option; did you use that as well? If you didn't request suboptimal tracebacks in the first place, that could be an obvious and fairly uninteresting explanation.
If you're interested in replicating their results exactly, I suppose your best bet is to contact IDT and ask them exactly what version of UNAFold and what options they use.
Hope this helps!
Statistics: Posted by nmarkham — Tue Feb 20, 2024 4:40 pm
