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Journal of Computational Biology
Genome Phylogeny Based on Short-Range Correlations in DNA Sequences
To cite this article:
Manuel Dehnert, Rainer Plaumann, Werner E. Helm, Marc-Th. Hütt.
Journal of Computational Biology.
June 2005,
12(5): 545-553.
doi:10.1089/cmb.2005.12.545.
Published in Volume: 12 Issue 5: June 13, 2005
Manuel Dehnert Bioinformatics Group, Department of Biology, Darmstadt University of Technology, D-64287 Darmstadt, Germany. Rainer Plaumann Mathematics and Science Faculty, University of Applied Sciences, D-64295 Darmstadt, Germany. Werner E. Helm Mathematics and Science Faculty, University of Applied Sciences, D-64295 Darmstadt, Germany. Marc-Th. Hütt Bioinformatics Group, Department of Biology, Darmstadt University of Technology, D-64287 Darmstadt, Germany. The surprising fact that global statistical properties computed on a genomewide scale may reveal species information has first been observed in studies of dinucleotide frequencies. Here we will look at the same phenomenon with a totally different statistical approach. We show that patterns in the short-range statistical correlations in DNA sequences serve as evolutionary fingerprints of eukaryotes. All chromosomes of a species display the same characteristic pattern, markedly different from those of other species. The chromosomes of a species are sorted onto the same branch of a phylogenetic tree due to this correlation pattern. The average correlation between nucleotides at a distance k is quantified in two independent ways: (i) by estimating it from a higher-order Markov process and (ii) by computing the mutual information function at a distance k. We show how the quality of phylogenetic reconstruction depends on the range of correlation strengths and on the length of the underlying sequence segment. This concept of the correlation pattern as a phylogenetic signature of eukaryote species combines two rather distant domains of research, namely phylogenetic analysis based on molecular observation and the study of the correlation structure of DNA sequences.  This paper was cited by:Generalized Whittle–Matérn random field as a model of correlated fluctuations S C Lim, L P Teo Journal of Physics A: Mathematical and Theoretical. Apr 2009, Vol. 42, No. 10: 105202 CrossRef The fractional oscillator process with two indices S C Lim, L P Teo Journal of Physics A: Mathematical and Theoretical. Mar 2009, Vol. 42, No. 6: 065208 CrossRef Evidence for Nonindependent Evolution of Adjacent Microsatellites in the Human Genome Miguel A. Varela, William Amos Journal of Molecular Evolution. Mar 2009, Vol. 68, No. 2: 160-170 CrossRef Informational structure of two closely related eukaryotic genomes Manuel Dehnert, Werner E. Helm, Marc-Thorsten Hütt Physical Review E. Sep 2006, Vol. 74, No. 2 CrossRef
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