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.
Sitnikova
T L
TL
Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk.
Zharkikh
A A
AA
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