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The base pair similarity score for two H-type pseudoknots p i(x) and p j y) in sequences Seq x and Seq y, respectively, is the sum of base pair similarity scores for the core pseudoknot stems as well as the base pair similarity score from a gapped local alignment of the recursive secondary structure elements in the loops (as described for multiloops).
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Another approach based on integer programming was proposed to predict the MFE secondary structure with recursive pseudoknots (Poolsap et al., 2009).
The proof shows that the leftmost sequence of base pairs given by the recursive construction of the random secondary structure has length at most O log n/ log log n) with high probability.
But the problem is recursive, because the proteins coded for by the "secondary" genes are, in turn, affected in their rates of activity by yet other proteins and so on until all the genes in the genome become included in the "partial" genotypic description.
It's all so recursive!
It's recursive, an infinite regress.
The movement is complex and recursive.
Instead, they ride a recursive current.
Such self-referential structures have recursive definitions.
They described their method as a "recursive incentive structure".
There is just a recursive loop of woe.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com