Statistical analysis of L-tuple frequencies in eubacteria and organelles.
This work is an attempt to study the structural features and evolutionary patterns of nucleotide sequences by analyzing their 1- through 4-plet frequencies and statistical relations between them. We present mathematical apparatus for this analysis. In particular, we introduce criteria to estimate the degree of homogeneity of L-plet composition in a given set of sequences and the dependence of the L-plet frequencies on the composition of lower orders. We apply these criteria to the study of eubacteria, mitochondria and chloroplasts. We demonstrate that L-plet frequencies are quite useful for revealing evolutionary relationship between DNA sequences and that the non-random distribution is more typical for doublets than to triplets. Non-randomness of triplet composition is more characteristic to coding than to non-coding regions, while no significant differences in dinucleotide composition can be observed. The obtained results can be used for revealing possible mechanisms of the codon usage phenomena.
Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk.
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Sitnikova
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Zharkikh
D000704:Analysis of Variance; D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D001699:Biometry; D003062:Codon / Q000235:genetics; D004247:DNA / Q000235:genetics*; D005822:Genetic Vectors; D008433:Mathematics; D015388:Organelles / Q000737:chemistry*
D003062:Codon; D004247:DNA