Sentence examples for external pairs from inspiring English sources

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).

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 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.

Here, only external base pairs are considered to measure accuracy.

The accuracy was measured by sensitivity, PPV and F-measure such that only external base pairs are considered.

Note that the third term describing sum of scores of external base pairs is multiplied by a positive weight parameter α.

In rip1, hybrids were immediately decomposed into individual external base pairs and their associated interior loops, so that individual hybrids were not tractable in a straightforward manner.

As suggested by Alkan et al. (2006), we set α ∈ (0, 1) so that external base pairs are less likely to be formed than internal ones.

PETcofold [ 18] employs covariance information in the internal and external base pairs to predict SSIR of two multiple alignments of RNA sequences.

compute the score matrices of the IP objective function for internal and external base pairs; solve the IP problem to predict the optimal joint secondary structure.