High evidence interactions not included in hybrid-ss-min fold

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JP
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Joined: 08/28/2019

Hello,

I am hoping you can give some insight into an issue I am experiencing with hybrid-ss-min. When I run hybrid-ss-min with just 1 contsraint, e.g:

F 3998 5059 5

This constraint is not included in the folded result. It seems when I choose any constraint more than 300bp apart it is not included. I have manually checked the base pairing of these nucleotides, and manually set the --maxbp option. Have you ever noticed this behaviour before?

Any help / advice would be greatly appreciated.

Many thanks,

Jon

NMarkham
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Joined: 09/29/2011
I just created a simple

I just created a simple sequence consisting of 200 repeats of CG, and observed the expected results with hybrid-ss-min 4.0.0. That is, if I add a constraint like "F 1 320 5", bases 1-5 pair with bases 320-316, for a somewhat less optimal folding.

What version of UNAFold do you have? There was a bug involving force constraints fixed with version 3.9a.

P.S. I apologize for being so late to respond to these questions!

JP
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Joined: 08/28/2019
thanks for your reply - not a

thanks for your reply - not a problem.

$ hybrid-ss-min -V

hybrid-ss-min (OligoArrayAux) 3.8
By Nicholas R. Markham and Michael Zuker
Copyright (C) 2006
Rensselaer Polytechnic Institute
Troy, NY 12810-3590 USA

NMarkham
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Joined: 09/29/2011
That explains it. I just

That explains it. I just dusted off a copy of version 3.8 and observed the same bug you did.

I believe your license should give you the right to download UNAFold 3.9a from iBridge, which fixes this and a handful of other fairly minor bugs as well.

JP
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Joined: 08/28/2019
Thank you very much for the

Thank you very much for the reply, I will investigate this with the new version.

JP
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Joined: 08/28/2019
positive energy structure

Will hybrid-ss-min ever output a structure with positive free energy?

NMarkham
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Joined: 09/29/2011
Potentially, yes.

Potentially, yes. hybrid-ss-min finds the MFE assuming at least one basepair, and a structure that has that free energy. Under certain conditions, such as high temperatures or pathological sequences, the best possible structure may still have positive free energy, i.e. be less stable than the unstructured state.