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Author Topic: can i get the cross_chain base-pair as a dot-bracket notation just use dssr  (Read 2174 times)

Offline langmei

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hi,
 I want to get the interaction base pair across the chain, but the dssr default output is the  base-pair of the whole the sequence ,can i use a optation to get the cross-chain interaction of two chain?
 thanks!

Offline xiangjun

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I get what you're saying, but I'm having trouble imagining how the requested new feature would be used. Please give specific examples to demonstrate what you're trying to accomplish.

Best regards,

Xiang-Jun

Offline langmei

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I will use the new feature to predict the base level interaction of two chain, so i need to obtain the cross chain base_pair notation (not include the inter chain inter chain base interaction)

Offline xiangjun

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Only two chains? How about more than two chains? What do you mean by "the cross chain base_pair notation"?

Offline langmei

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all the chain interaction in one pdb file, i want to get the dot-bracket of cross chain interaction. thank you!

Offline xiangjun

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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.

Offline langmei

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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)

Offline xiangjun

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

Offline langmei

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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;



Offline xiangjun

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Code: [Select]
X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;

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

Offline langmei

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this not dot-bracket notation , i want to get the dot-bracket notation just contain the above cross chain pairs.

Offline xiangjun

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Please pay close attention to my requests for clarification.

Offline xiangjun

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As a followup, DSSR Pro now has the option to derive only pairs across chains.

 

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.