If by the result of the operation the k-mer should be included in the output set, its final count is calculated by predetermined rule and the k-mer is written to the output list.
Using a 1-bp sliding window the frequency distribution of each k-mer should be normally distributed, with deviations from this a result of heterozygosity, sequencing error, and repeat regions in the genome.
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.
To avoid information loss, as many as possible patterns (or k-mers) should be considered.
For any l where 4 l exceeds twice the genome size, most l-mers should be unique [ 19].
Note that the presented construction (Section "Construction algorithm") is inherently off-line, as all k-mers should be known before the data structure is built.
These ultra-frequent n-mers should be useful as high density markers in the genome and as primers for assays such as random amplified polymorphic DNA (RAPD) [ 18] in which a large number of regions of the genome may be amplified in a single PCR reaction.
Thus to compare genomes (or protein sequences) based on similarity measures [see Equations (3) and (5)] that use frequency distribution vectors [see Equation (2)] the k-mer size should be chosen in such a way to satisfy the inequality shown in Equation (15).
They resolve the problem based on the assumption that, although the multiplicities of these erroneous k-mers are high, their multiplicities should be lower than the nearby correct k-mers.
However, when constructing the k-mer index, occmin and occmax should be chosen carefully.
