Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Author Topic: base-pair in dot-bracket notation in dbn file  (Read 949 times)

Offline langmei

  • non-commercial
  • with-posts
  • *
  • Posts: 7
    • View Profile
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?

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1611
    • View Profile
    • 3DNA homepage
Re: base-pair in dot-bracket notation in dbn file
« Reply #1 on: July 09, 2021, 09:10:54 am »
Quote
why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete?

DSSR derives all base pairs (including noncanonical ones) in a given coordinate file. The .dbn output is for 2D structure with canonical pairs only.

Please read the 2015 NAR paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" thoroughly, perhaps several times, to gain a better understanding of the fundamentals. See also the post "Reproducing results published in the DSSR-NAR paper" and links therein.

Best regards,

Xiang-Jun
« Last Edit: July 09, 2021, 09:35:36 am by xiangjun »

 

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.