  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.
