Web Site • Request for Assistance with Server Performance
Hello,I trust this message finds you well. I'm reaching out to discuss a recent concern regarding server performance.In the past few days, the computational tasks of UNAFold(especially DINAMelt...
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Web Site • Re: Request for Assistance with Server Performance
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...
View ArticleUNAFold • Two Strand DNA Structure annealing
Dear UNAFold teamI was wondering if its somehow possible to enter a top ssDNA and a separate bottom ssDNA strand to predict structures for dsDNA oligo annealings.Ive separated so far the two strands...
View ArticleUNAFold • Re: Two Strand DNA Structure annealing
What command(s) are you using?I have a hunch you want to use hybrid-min instead of hybrid-ss-min.Statistics: Posted by nmarkham — Fri Nov 03, 2023 12:00 am
View ArticleUNAFold • Melting Temperatures DNA oligos (DINAMelt)
Hello,I am a member of the Small Biosystems Lab (University of Barcelona), led by Prof. Felix Ritort. Over the years, we have used the mFold server to compare with the results obtained in...
View ArticleUNAFold • Re: Melting Temperatures DNA oligos (DINAMelt)
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...
View ArticleUNAFold • Discrepancies between UNAFold softwares
Hello,I recently obtained the UNAFold license from Rensaeller and I noticed that there was occasionally discrepancies between this software and the IDT version found at...
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UNAFold • Re: Discrepancies between UNAFold softwares
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...
View ArticleWeb Site • Error in DINAmelt
There is an error whenever I try to use homodimer simulations and hybridization of two different strands. It doesn't matter what conditions I use, I always get this error: Error in hybrid2.cgiThank...
View Articlemfold • Ionic conditions
Hi! I'm having some trouble understanding what the ionic conditions stand for in MFold. Since we only provide the DNA sequence, how are the calculations made? Does MFold only consider one molecule in...
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