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Fig. 7 | BMC Bioinformatics

Fig. 7

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

Fig. 7

The effect of restricted unpaired bases is shown with an example of an RNA sequence from the tRNA family. If the three bases on the 3’ end of the sequence are free to pair they form pseudoknotted base pairs (b) to lower the energy of the structure, therefore causing loss of the cloverleaf shape known within the tRNA family, and deviation from the reference structure. However, once the three bases are identified as restricted unpaired and forced as such (presented as dark filled bases at the 3’ end of part (a)) the reference structure is correctly predicted (a)

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