Lattice-Automation / seqfold

nucleic acid folding
MIT License
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folded structure is not the same size of the input sequence and differs significantly from mfold prediction #14

Closed ita-infiniplex closed 1 year ago

ita-infiniplex commented 1 year ago

For example:

from seqfold import fold, dot_bracket, dg 
seq = 'AAAAAAAAAAAGGCCCCCTCTCTTGC'   
structure = dot_bracket(fold(seq))                    
energy = dg(seq) 
len(seq) != len(structure)            # 26 != 19
structure == '..........(((...)))'
energy == 0.4

RNAFold structure: image with dG: -0.95

and mfold structure: image with dG: -0.27

Am I using it wrong or is something off here?

Thanks!