Non-alignment comparison of human and high primate genomes
  Compositional spectra (CS) analysis based on k-mer scoring of DNA sequences was employed in this study for dot-plot comparison of human and primate genomes. The detection of extended conserved synteny regions was based on continuous fuzzy similarity rather than on chains of discrete anchors (genes or highly conserved noncoding elements). In addition to the high correspondence found in the comparisons of whole-genome sequences, a good similarity was also found after masking gene sequences, indicating that CS analysis manages to reveal phylogenetic signal in the organization of noncoding part of the genome sequences, including repetitive DNA and the genome "dark matter". Obviously, the possibility to reveal parallel ordering depends on the signal of common ancestor sequence organization varying locally along the corresponding segments of the compared genomes. We explored two sources contributing to this signal: sequence composition (GC content) and sequence organization (abundances of k-mers in the usual A,T,G,C or purine-pyrimidine alphabets). Whole-genome comparisons based on GC distribution along the analyzed sequences indeed gives reasonable results, but combining it with k-mer abundances dramatically improves the ordering quality, indicating that compositional and organizational heterogeneity comprise complementary sources of information on evolutionary conserved similarity of genome sequences. 
V.M. Kirzhner, S. Frenkel, A.B. Korol
q-bio.GN