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RNA structures (DSSR) / Non canonical RNA pairs in bpseq format
« on: December 01, 2018, 01:40:23 am »
I am working on RNA secondary structure predictions problem using deep learning. For that I need  RNA contact map which include all kind of possible pairs. I am using x3dna-dssr to get RNA secondary structure.  Is there any possible way to get to both canonical and  non canonical pairs of  RNA in bpseq format using DSSR software as .bpseq and .ct output file do not contains non canonical pairs? 

I am bit confused about the notation used in the output file which consists of both canonical and non canonical pairs. In the manual, it is mention that 'A.G19' means guanosine #19 on chain ‘A', but the output file that I got for '1hr2' RNA, nt index is off-set by some number. In the output file for this RNA index of first pair is A.U106 and A.G215. Here first two notation are fine. But notation third is 106 and 215 is off-set by some number. I have attached output file that I got for '1hr2' RNA.


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