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Messages - mahfuz

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1
I'm extremely sorry that I haven't seen it before. I think
Quote
The dot symbol denotes cases where edges or orientations cannot be defined (see bp #7 in the list of base pairs on Page 14, and Figure 5(D)).
is my answer.

2
Thank you so much. I've another query. In the base-pair list I found the following symbols which I understand: cWW, tWW, cSH, tSH, cHS, tHS

But I cannot be able to get the meaning of c.H, t.H, c.S, t.S, c.W, t.W - what is the . (dot) here? Can you please explain me.

Sorry for asking so many questions.

Thanks.

3
Thank you for your quick response. I was just trying to compare the outputs from MC-Annotate, RNA-View and DSSR. There is something 'adjacent' and 'non-adjacent' stackings showing in MC-Annotate. I mistakenly wrote 'canonical and non-canonical' for these terms. I'm extremely sorry for my mistake.

Can you please help me to compare the 'adjacent and non-adjacent stacking' of MC-Annotate output with something in DSSR output?

Thanks

4
RNA structures (DSSR) / Seeking help with DSSR (Base Pair and Stacking)
« on: October 05, 2018, 05:49:11 pm »
Hi Dr. Xiang-Jun Lu,

I'm working on your annotation tool DSSR and trying to get the base-pair and stacking information from DSSR annotation. The base-pair part is clear enough but I'm facing problem for finding the stackings. The canonical and non-canonical stackings are not clear to me. I'm also trying to get the direction of the stackings (upword/downword/inward/outward).

Thanks

Mahfuz

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.