Messages

1

RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)

« on: October 15, 2018, 12:29:15 pm »

I'm extremely sorry that I haven't seen it before. I think

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

RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)

« on: October 12, 2018, 05:48:04 pm »

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

RNA structures (DSSR) / Re: Seeking help with DSSR (Base Pair and Stacking)

« on: October 09, 2018, 12:16:56 pm »

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