The underlying problem is unlikely to be solved by more sequencing: for example, the breast-cancer-associated genes BRCA1 and BRCA2 have been sequenced in over a million patients and yet a high proportion of returned results continue to be VUS.
Fig. 2 Demonstration of the prototype swap for a sample initial solution for N = 5000 data vectors from k = 15 clusters (data set S2). On the other hand, the correct locations of the prototypes can be solved by a sequence of prototype swaps, and leaving the fine-tuning of their exact location to k-means.
By transforming protein local backbone conformations into a conformational alphabet [34], it converts geometric structural comparison problems into string comparison problems that can be solved by conventional sequence alignment algorithms.
The functional fragments recognition problem can be solved by finding sequences in which the words from a given pattern are overrepresented.
Some of these problems might be solved by the complete sequencing method, but this technology is still too expensive for large studies.
Ultimately, this coverage issue will be solved by whole genome sequencing studies, but these remain too expensive for widespread use.
Apparently this problem cannot be solved by the current sequencing technology using short reads and paired-end information of reads can only partially alleviate the problem.
Nowadays, a natural and popular approach is trying to find some suitable approximations of an MPCC so that it can be solved by solving a sequence of nonlinear programs.
Thus, the problem (6) can be solved by searching a sequence in the set (mathcal {V}_{m}), (boldsymbol {y}_{i}in mathcal {V}_{m}, i=1,cdots, N), owing the following properties.
While our current hypothesis still reveals a few branches lacking in robustness – a problem that will most likely be solved by adding more sequence data from currently under-represented species – our analysis nonetheless puts forward several well corroborated hypotheses concerning seed plant phylogeny, namely: Gymnosperms are a monophyletic group, sister to the angiosperms.
