In addition, to evaluate the difference between two structures, we used the base pair distance (dBP) (Gruber et al. 2008), given by the number of base pairs not shared by them.
To test whether nucleotide composition heterogeneity could lead to the observed differences in positive selection between secondary structures, we analyzed simulated data sets generated in such a way that the only difference between the regions with different structure was their nucleotide composition.
As a result, in addition to these technical problems causing nonlinear relationships between sequences and structures, we propose that there exists a more fundamental reason: besides PNI, the number of indels is another independent variable that contributes to structure variations in evolution.
To facilitate studies on the neural communication between connected brain structures, we developed a multi-electrode microdrive for chronically recording ensembles of neurons in two different brain areas simultaneously.
We have been active participants in these transformations [24], [27], [28], and like many others concluded that in order to bridge the fragmentation between distinct data structures, we needed to break down the data structures themselves[20], that is, to reduce the interoperable elements to RDF triples[29].
To clarify the relationship between the two structures, we counted the number of anaphase cells showing UFBs and/or chromatin bridges after replacement of endogenous PICH by either PICH-WT or PICH-WAB (Fig. 4).
To determine the motion best describing the transition between the two crystal structures, we performed a normal mode analysis on the El Némo server [31] using the two structures.
Using the ViennaRNA function to calculate dBP between two ensembles of structures, we calculated d0, as well as d1 and de (see later).
Rather than quantifying the explicit difference between predicted minimum free energy (MFE) structures, we consider the difference of the distribution of structures.
To determine evolutionary distances between organisms simultaneously on sequences and secondary structures we used Profile Neighbour Joining (PNJ) [ 76] as implemented in ProfDistS 0.98 [ 77, 78].
