Alignment and folding with the original structure and alignment dependencies of Sankoff requires substantially different recursions.
The growth behavior, alignment nature, substrate dependency, size and shape control, fabrication of the field-effect transistors, and the temperature-dependent electrical transport of the single ZnO nanorods used in this study have been reported in detail in our previous works [21 24].
A third limitation of our approach, and more generally of all covariation analysis methods based on a multiple sequence alignment, is the dependency on the alignment quality.
Data of each team member is processed to derive the sub-group network which captures who was for how long in a sub-group with another team member, as well as the movement alignment network, which captures dependencies in activity levels between team members.
(Sankoff's Dependencies Between Alignment and Structures).
D efinition 1 (Sankoff's Dependencies Between Alignment and Structures).
This means that any complexity in the geometry will increase the dependency of the alignment between machine and cross-machine direction which in turn, will reduce the tolerance of the alignment.
Finally, we have shown possible solutions to alleviate the effects of a strong guide-tree dependency, which include iterative alignment reconstruction, use of consistency across different alignments and trimming.
We used ungapped alignments here to avoid any dependency of the results on the value of gap penalty.
Economic dependency favors a political alignment.
For each alignment tool, Figure 4 shows the dependency of alignment quality on sequence identity across k2; for each benchmark instance, the quality is measured as similarity to the Rfam-derived reference alignment reported as sum-of-pairs score (SPS) by compalignp (Wilm et al., 2006).
