UNAFold

I apologize for not responding to this at the time it happened. The server seems fine now (unsurprisingly).

We did have some chronic issues that we think we've resolved, so hopefully this won't happen again.

In general, if you want suboptimal structures, you use the "--mfold" option. Merely specifying it engages "mfold mode", where hybrid-ss-min (or hybrid-min or hybrid-intra-min, for that matter) generates a sample of suboptimal structures as well as an optimal one. However, --mfold...

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 th...

I apologize for not seeing this message sooner! The DNA parameters have not changed with UNAFold 4.0 (although the RNA parameters have). If I recall correctly, the Owczarzy data set was our primary reference when UNAFold was originally developed. I dug up what I think are those melting profiles and ...

What command(s) are you using?

I have a hunch you want to use hybrid-min instead of hybrid-ss-min.

Hi Yuki,

I killed a couple of long-running processes that I think were causing issues on the server. Performance seems good again to me.

Thanks for letting us know. I'll pester Michael again about solving the underlying problem.

Nick

I'm sorry to hear this, but I'm afraid it's out of my hands. RPI controls licensing for UNAFold, and I have no say in when or even if they respond to such a request.

When I first read this question I was convinced there must be a flag to change the dimensions of a plot, but there doesn't seem to be. It seems that Postscript plots can only be generated at 13 inches by 17 inches. Raster images can be created at any desired size, but the aspect ratio is unchanged. ...

This is puzzling. I should be clear that I am not the author of mfold_util, but I'm fairly confident there are no limitations like what you described. I wonder if you can download this binary: http://www.unafold.org/for-julie/sir_graph_ng and try it in place of the one you have. It's statically link...

The fact that you've written them all with 5' at one end and 3' at the other suggests to me that they're linear. However, they're your sequences, not mine so only you know for sure!