Identifying characteristic scales in the human genome.
The scale-free, long-range correlations detected in DNA sequences contrast with characteristic lengths of genomic elements, being particularly incompatible with the isochores (long, homogeneous DNA segments). By computing the local behavior of the scaling exponent alpha of detrended fluctuation analysis (DFA), we discriminate between sequences with and without true scaling, and we find that no single scaling exists in the human genome. Instead, human chromosomes show a common compositional structure with two characteristic scales, the large one corresponding to the isochores and the other to small and medium scale genomic elements.
Carpena
P
P
Departamento de Física Aplicada II, Universidad de Málaga, 29071 Málaga, Spain.
Bernaola-Galván
P
P
Coronado
A V
AV
Hackenberg
M
M
Oliver
J L
JL
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D020451:Contig Mapping; D004252:DNA Mutational Analysis / Q000379:methods*; D005815:Genetic Code / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D040641:Quantitative Trait Loci / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*