Sentence examples for structure of the alignment from inspiring English sources

3) Folding energy of the consensus secondary structure of the alignment computed by RNAalifold (consmfe ).

Second, we modified the data structure of the alignment graph to store the orientation between matching segments so that we could detect inversions.

A base pair (i, j) is contradicting if there exists a base pair (p, q) in the reference structure of the alignment, such that i < p < j < q or p < i < q < j.

At the end of fragment chaining step, a tentative chain is obtained that represents the general structure of the alignment, yet overlap split positions are not exactly specified in the resulting chain.

20 In predicting the consensus secondary structure for a multiple sequence alignment, a predicted base pair (i, j) is inconsistent if column i in the alignment is paired with column q, q ≠ j, or column j is paired with column p, p ≠ i, and p, q form a base pair in the reference structure of the alignment.

Direct comparison of the sampled consensus structures is impractical because of the dependence of the indices of the bases of sampled structures on the alignment.

Figure 7 presents the structure of the reference alignment, as well as alignments generated by MSARC, Probalign and MSAProbs.

For the structure component of the alignment, we used BRCA1 RING NMR structure 1JM7.pdb and the BRCA1 BRCT repeat crystal structures 1JNX.pdb and 1T29.pdb [ 28- 30].

The general mosaic structure of this alignment is not consistent with a model in which evolution is happening with equal frequency along the length of the protein.

Finally, the length and structure of the RDP alignment changes as new reference models are included.

In the RNA model setups, a third partition is defined, according to the consensus secondary structure of the whole alignment and all paired position are extracted and pooled in third partition.