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Fig. 5 | BMC Bioinformatics

Fig. 5

From: KnotAli: informed energy minimization through the use of evolutionary information

Fig. 5

Illustration of the main recursions of restricted pseudoknotted energy minimization step KnotAli. The sequence is represented as a line with bases as index positions; solid arcs indicate base pairs and dashed arcs enclose areas containing unconsumed structure. Red circles represent fixed end points of a region. Blue squares are unpaired indices. We represent the base pairs of the guide structure on top to distinguish then from the predicted base pairs in energy minimization steps of KnotAli shown in the bottom of the line

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