In particular, we make use of posterior probabilities such as base-pairing probabilities and hybridization probabilities for scores of internal pairs and those of external pairs, respectively, to incorporate further structural information into the objective function as in the case of LARA (Bauer et al., 2007).
rip calculates exact base-pairing probabilities of internal base pairs and external base pairs by taking O(n) time and O(n) space where n is the length of the longer sequence.
Wherever any of these programs required access to external pairing-posterior probabilities, we used ViennaRNA v1.7 (Hofacker et al., 1994).
Accordingly, it uses the approximate information of the internal and external base pairing probabilities of joint structures as an objective function of integer programming.
Given secondary structure S, an external base pair is a base pair (i, j) ∈ S, which is not interior to any other base pair of S; i.e. there is no (x, y) ∈ S with the property that x < i < j < y.
Importantly, the alignment A and the structures S and T are not independent of each other: Sankoff requires that all external base pairs and interior base pairs of multiloops of both RNAs are covered by (S, T, A ).
In this study, we fix α = 0.5, that is, external base pairs contribute to the objective function by half compared with internal base pairs.
We compared RactIP with rip, which samples joint structures from internal and external base-pairing probabilities, and RactIP combined with rip, in which internal and external base-pairing probabilities calculated by rip were used in the IP [see Equation (5)] instead of factorized ones.
We use a partial correlation approach, i.e. parametrize the set of admissible controller - external input pairs by a finite set of matrix-valued trigonometric moments.
An alternative to AC dielectrophoresis is the insulator-based DEP (iDEP) or DC DEP [5, 13, 14], in which no metal microelectrodes are embedded in the chip and DC electric fields are applied from an external electrode pair.
Here, only external base pairs are considered to measure accuracy.
