Four different attributes were calculated for each reference alignment, which reflect the overall difficulty of the alignment: the total number of sequences to be aligned, the average length of the sequences to be aligned, the norMD score which is an objective function for MSA based on the Mean Distance (MD) scores introduced in ClustalX [63].
As many false SNP were located at the splice sites due to the difficulties of alignments near indels (splicing sites), they were removed from the final set.
In addition, an intraspecies alignment tends to be less accurate than an interspecies one, due to the difficulty of computing alignment scores corresponding to the actual divergence time [ 52].
That highlights the difficulty of continuous alignment of two different systems.
In order to reduce difficulty of optical alignment in developing phases, while increasing robustness, IR2-OPT employs a rather simple design: a triplet of ZnS (G1), quartz (G2), and quartz (G3).
Furthermore, the tolerance of misalignment existing in inter-ONUs traffic is investigated and analyzed for all-optical encoding operation, and the difficulty of pulse alignment is proved to be lower.
Sdev and Smod results within each similarity range are consistent across most alignment methods (Fig. 2), pointing to the inherent ease or difficulty of aligning particular domains.
Computational difficulty of biological network alignment becomes apparent when we need to align a query network with a database of biological networks.
Nakashima et al. reported three cases of osteoporotic vertebral fracture complicated by Parkinson's disease, all of which showed significant deterioration of sagittal alignment due to postoperative compression fracture or sinking of the fusion cage, suggesting the difficulty of maintaining sagittal alignment even with posteroanterior surgery [ 13].
