Such result would look very similar to a decision tree, and the corresponding k-mers could be related to the notion of crowns (see [ 79]).
On the other hand, identical k-mers could be derived from physically, functionally, or evolutionarily different regions of the genome and are therefore not homologous (k-mer homoplasy).
Although these short-mers could be explained by lack of capping, we believe that they actually derive from chain extension of residual amidate building block 11 after OSN.
Another possible improvement is that long singly linked lists of k-mers could be replaced by a more sophisticated structure such as a hash table or some sort of tree (Giladi et al., 2002).
To address this question, we aligned siRNA sequences and observed that 5 of 25 sequences (20%) among 12-mers and 3 of 22 sequences (13.6%) among 13-mers could be found from longer siRNA sequences (Additional file 5).
In the same spirit as the k-mer reordering we described under optimizations already implemented (Supplementary Material), some subset of 'pier' k-mers could be stored in a smaller, more rapidly accessible data structure as proposed in Cao et al. (2004).
In order to do this, we must choose an oligo length long enough that there are some n-mers that do not appear in the human genome (i.e., > 13-mers), and long enough that some non-human n-mers are likely to appear in non-human organisms, yet short enough that that a large fraction of the non-human n-mers could be probed in a human sample (i.e., < 16-mers).
Considering the accuracy of the MRI-based target, the period of MER could be shortened by starting recording at 6-mm instead of 8-mm distance from the MRI-based STN target and 100-mm instead of 12-mm distance from the MRI-based ventral border of the GPi.
(Sets of 3-base 19-mers were used, because a 19-mer is representative of commonly used hybridization probes, and analysis of k = 3 19-mer sequences could be performed on a modern portable computer).
