Correlation property of length sequences based on global structure of the complete genome

Abstract

This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time L are used to discuss the correlation property of these sequences. The values of the exponents from these methods of these three kinds of length sequences of bacteria indicate that the long-range correlations exist in most of these sequences. The correlations have a rich variety of behaviors including the presence of anti-correlations. Furthermore, using the exponent gamma, it is found that these correlations are all linear (gamma=1.0+/-0.03). It is also found that these sequences exhibit 1/f noise in some interval of frequency (f>1). The length of this interval of frequency depends on the length of the sequence. The shape of the periodogram in f>1 exhibits some periodicity. The period seems to depend on the length and the complexity of the length sequence.

Universal power law behaviors in genomic sequences and evolutionary models

“…For these reasons, in our analysis we decided to construct strictly disjoint subsets of exons, according to their position in the transcript (5'UTR exons, protein coding exons or 3'UTR exons) 3 . Moreover, we created a non redudant genome-wide datasets of exons, considering only one isoform for each gene, the most extended one.…”

“…A typical example was the identification more than ten years ago of long range correlations in the base composition of DNA (see for instance [1,2] and references therein). With the availability of complete sequenced genomes, the correlation property of length sequences has been studied separately for coding and non coding segments of complete bacterial genomes, showing a rich variety of behaviour for different kinds of sequences [3,4]. This line of research has been recently extended to the search of similar universal distribution for more complex features of eukaryotic DNA sequences like for instance 5' untranslated regions (UTR) lengths [5], UTR introns [6] or strand asymmetries in nucleotide content [7,10].…”

Multifractal characterization of complete genomes

“…Some results on the classification and evolution relationship of bacteria were found in [16]. The correlation property of length sequences was discussed in [17].…”

Analysis of global geomagnetic variability

“…The DFA method has been applied successfully in diverse fields such as DNA sequences, heart rate dynamics, neuron spiking, weather records, economics time series (Kantelhardt et al, 2002, and the references therein). Yu et al (2001) used it to study the length 702 V. Anh et al: Analysis of global geomagnetic variability sequences of complete genomes. Recently, Yu et al (2006) used the DFA method to study the classification problem of protein secondary structures.…”