Dispersion of chromosome coverage by latent periodicity regions for the D. melanogaster genome is comparable with that for S. cerevisiae.
For each training data set in the six model species, the relative coverage of periodic region R was calculated for 253 individual amino acid periodicities as feature vectors for SVM input.
For amino acid periodicity, we calculated the relative coverage of the periodic region (R) of each training set (i) with 253 patterns of amino acid periodicities (j): 23 amino acid groups × 11 kinds (2, 3, 5, 7, 8, 9, 11, 13, 15, 17, 19 periods): where P is the length of periodic region of periodicity j in a single protein i, and N is the full amino acid length of a single protein i.
Comparing Tables 2 and 4, one can see that the shares of nucleotides, located in the genes, for all organisms in the HeteroGenome are practically similar to the shares of genome coverage by the regions of latent periodicity.
Because of nonredundancy of the results of the approach, for each genome under consideration we can estimate its coverage as a percentage of latent periodicity regions, and with the aid of a special parameter, which is described in the next section, we can analyze the conservation of periodic structure in the regions.
Thus, sequences representing the groups form nonredundant chromosome coverage by regions of reliable heterogeneity (latent periodicity).
The diffraction pattern consists of a periodic distribution with a periodicity reciprocally related to the raster periodicity.
An important quantitative index used to study the evolution and functional meaning of latent periodicity regions in genomes is the amount of genome coverage by these regions.
The theory of infectious diseases predicts that outbreak periodicity is mainly driven by birth rates and vaccine coverage [ 18, 19, 22].
Analysis of the HeteroGenome data distribution over functional (annotated in GenBank) and nonfunctional (unassigned) genome DNA sequences shows that the share of latent periodicity in the genes is similar to the general genome coverage by the regions of latent periodicity.
