Messages

1

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 12, 2021, 07:59:07 am »

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

2

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 12, 2021, 02:16:06 am »

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;

3

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 11, 2021, 11:15:51 pm »

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)

4

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 11, 2021, 09:16:55 pm »

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

5

RNA structures (DSSR) / Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 09, 2021, 09:50:43 am »

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)

6

RNA structures (DSSR) / can i get the cross_chain base-pair as a dot-bracket notation just use dssr

« on: July 09, 2021, 04:54:18 am »

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!

7

RNA structures (DSSR) / base-pair in dot-bracket notation in dbn file

« on: July 09, 2021, 04:47:56 am »

hi,
   why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete? for example:
 in RNA with id "2YIE", dot-bracket notation file consists of 32 base-pairs as shown below:
>2YIE nts=112 [2YIE] -- secondary structure derived by DSSR
gGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAUCCAU&gGAUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUCG&?
((((((((......(((.......))).[[((((((....[[))))...(((..&)))....(((((.......)))))]])).(((....]]))).......)))))))).&.
but if you extract base-pair from .json file, then there are 50 base-pairs in this RNA as shown below:
['X.GTP1', '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.G10', 'X.G47']
['X.G12', 'X.C31']
['X.G12', 'Z.G93']
['X.C13', 'X.G28']
['X.A14', 'X.G28']
['X.G15', 'X.C27']
['X.G16', 'X.C26']
['X.G17', 'X.C25']
['X.U18', 'X.A22']
['X.G19', 'Z.A90']
['X.A29', 'Z.U94']
['X.C30', 'Z.G93']
['X.C31', 'Z.G84']
['X.G32', 'Z.C83']
['X.G33', 'X.C46']
['X.G33', 'Z.A104']
['X.U34', 'X.A45']
['X.G35', 'X.C44']
['X.G36', 'X.C43']
['X.U37', 'X.A40']
['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.GTP57']
['Z.G62', 'Z.C83']
['Z.G62', 'Z.G84']
['Z.U64', 'Z.A80']
['Z.U65', 'Z.A79']
['Z.U66', 'Z.A78']
['Z.G67', 'Z.C77']
['Z.G68', 'Z.C76']
['Z.U69', 'Z.A73']
['Z.A85', 'Z.G98']
['Z.C86', 'Z.G97']
['Z.A87', 'Z.U96']
['Z.G88', 'Z.C95']
['Z.U89', 'Z.A92']

why there are many base-pair in the dssr-2ndstrs.dbn file?