In this experiment, we used D933-mer, rather than D333-mer, to provide a large enough difference between the mass of our test peptide and that of an unlabeled 33-mer internal standard, thereby enabling quantitation.
The use of gapless, subsequence of length w enhances the filtering quality as we compare a w-mer rather than single nucleotide at a given index position.
This result is surprising and may seem counter-intuitive, as we have four filters to apply to the queried k-mer rather than a single filter as in [ 9].
Previous work indicated that a high molecular mass assembly (roughly a 12-mer), rather than low-order AβOs, is primarily responsible for the neuronal attack suffered by neurons exposed to AβOs.
Probably this is due to the limitations of antibodies, which have a shorter minimal recognition site (7-mer rather than the 9-mer T cell epitope) and may not be able to detect all amino acid substitutions.
Page 3: in the proposal of a new sensor and compute P (7-mer and SS), why to choose the 7-mer rather than 8-mer or 6-mer should be explained.
In general, the rules computed for distinct species do not seem to use disjoint, species-specific sets of k-mers, suggesting that discrimination critically depends on the frequency of a k-mer rather than on its simple presence or absence in a species.
The de-Bruijn graph is built based on the overlaps of length K-1 between these K-mers rather than the actual reads.
This is in spirit similar to the likelihood function used in other studies, except that this is the likelihood of observing sig-mers rather than fragments (Li and Dewey, 2011) or k-mers (Patro et al., 2013).
Secondary structure prediction of the spliced XBP1-BSL indicated that the newly generated CCG¦CAGC motif would be constrained in a 6-mer loop rather than the conserved 7-mer loop of the original splice junctions (Fig 1B).
