As was generally the case for BAliBASE, the DIALIGN score of the (biologically meaningful) anchored alignment was lower than the score of the (biologically wrong) default alignment.
The accuracy of anatomical limb alignment was lower for knees with greater femoral (odds ratio = 1.2) and tibial (odds ratio = 1.2) bowing.
This coincided with the finding that the SNP frequency of SR3 and wheat database EST (SR3 vs Ta alignment) was lower than those of the SR3 vs JN177 alignment (Table 2).
With this information, the alignment is accepted as statistically significant if the probability of finding such an alignment by chance is lower than a user-defined value (Karlin and Altschul, 1990).
It is obvious that the alignment score Xa - Ya is lower than the alignment score Xa - Yb, while the alignment ratio of Xa - Ya is the higher of the two.
However, in Hpr bones, this change in mineral particle alignment is much lower for the LB compared to wild type mice, indicating that abnormal mineralisation may therefore be associated with the impaired mechanical properties of muscles [28] in rachitic mice.
Therefore, the cost of an optimal flow in the network N′, obtained by removing such edges from N, equals to the cost of an optimal flow in N. Note that in the case of RNA tree alignment, removed edges correspond to pairs of subtrees which are sufficiently dissimilar so that their pruning cost is lower than their alignment cost.
However, if an estimated score of the multiple alignment between these m + 1 PPIs is lower than the score of the best multiple alignment found so far between all the K input PPIs (K ≤ m), we can ignore this combination of transformations and there is no need to try to extend it.
Moreover, another intron is present in the start codon of almost all genes in lancelet and of two genes in corals also supports this view, though the sequence conservation at the beginning of the coding region is lower and their alignment is more ambigous.
For the non-coding regions, the coverage of the human-mouse alignment by the pig genome sequences is lower than for the coding regions, but this may be explained by lower selective constraints and a much higher rate of insertions-deletions in these regions.
