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« **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?