Variations of the mononucleotide and short oligonucleotide distributions in the genomes of various organisms.
We calculated the variation coefficients of the mononucleotide and short oligonucleotide distributions in over 1700 long genomic sequences originating from six organisms to demonstrate that the human and Escherichia coli genomic sequences were the least and the most uniform, respectively. The most non-random genomic distributions were exhibited by the four canonical nucleotides, followed by the strong and weak nucleotides, while the distributions of purine or pyrimidine nucleotides and especially the distributions of (A+C) and (G+T) were significantly more uniform even in the human genome. In the human and mouse genomes, the highest coefficients of variation were further observed with the oligonucleotides where CG was combined with the strong nucleotides while its combination with the weak nucleotides significantly decreased the variation which, however, was still very high. High variation was also exhibited by the remaining oligonucleotides composed exclusively of the strong nucleotides or those containing only weak nucleotides. On the other hand, the distributions of oligonucleotides containing similar and especially the same numbers of the strong and weak nucleotides, but no CG or TA dinucleotide, were the most uniform. The information following from the present analysis will be useful not only in the identification of important genomic regions but also in computer simulations of the genomic nucleotide sequences in order to trace and reproduce the pathways of genome evolution.
Häring
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Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-61265, Czech Republic.
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D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D001330:Electronic Data Processing; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D016680:Genome, Bacterial; D016681:Genome, Fungal; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D051379:Mice; D009841:Oligonucleotides / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA
D009841:Oligonucleotides