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Questions and answers > RNA structures (DSSR)

can i get the cross_chain base-pair as a dot-bracket notation just use dssr

<< < (2/3) > >>

xiangjun:
Please give specific examples of what you want to accomplish so that others can assist you. It's also a good way to get your thoughts straight.

langmei:
OK, for example RNA 2YIE there are two chain as fellow：
>strand_X
gGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAUCCAU
(((((((((<..(.(((({..)..))))[[((((((({.)[[))))>.((((..
>strand_Z
gGAUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUCG
))))...((((((}..)..)))))]]))(((((}.)]])))).....))))))))).
the dot-bracket contain cross chain base-pair and inner chain base-chain. but i just need the base-pair that cross X and Z.(X and Z interaction)

xiangjun:
What the .dbn should be in this case (2YIE, between chains X and Z)?

langmei:
just contain the base pair x-z like fellow，not contain x-x or z-z。 it is clear？ maybe i can use the .json reproduce the result, but i do not know how to do.
X.g1 - Z.C112;
X.G2 - Z.U111;
X.A3 - Z.U110;
X.U4 - Z.A109;
X.C5 - Z.G108;
X.U6 - Z.A107;
X.U7 - Z.A106;
X.C8 - Z.G105;
X.G9 - Z.A104;
X.G12 - Z.G93;
X.G19 - Z.A90;
X.A29 - Z.U94;
X.C30 - Z.G93;
X.C31 - Z.G84;
X.G32 - Z.C83;
X.G33 - Z.A104;
X.A38 - Z.G70;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.A49 - Z.U60;
X.U50 - Z.A59;
X.C51 - Z.G58;
X.C52 - Z.g57;
X.G11 - Z.G84;
X.A29 - Z.G93;
X.C31 - Z.C83;
X.U42 - Z.C82;

xiangjun:

--- Code: ---X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;
--- End code ---

Are you sure this is the dot-bracket notation, with desired base-pairs you want???

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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.