Lack of biological significance in the 'linguistic features' of noncoding DNA--a quantitative analysis.

Recently, the application of two statistical methods (related to Zipf's distribution and Shannon's redundancy), called 'linguistic' tests, to the primary structure of DNA sequences of living organisms has excited considerable interest. Of particular importance is the claim that noncoding DNA sequences in eukaryotes display specific 'linguistic' features, being reminiscent of natural languages. Furthermore, this implies that noncoding regions of DNA may carry some new, thus far unknown, biological information which is revealed by these tests. In this paper these claims are tested quantitatively. With the aid of computer simulations of natural DNA sequences, and by applying the same 'linguistic' tests to both natural and artificial sequences, we investigate in detail the reasons of the appearance of the claimed 'linguistic' features and the associated differences between coding and noncoding DNAs. The presented results show quantitatively that the 'linguistic' tests failed to reveal any new biological information in (noncoding or coding) DNA.

A quantitative test of long-range correlations and compositional fluctuations in DNA sequences.

Recent findings concerning long-range correlations and fractals in intron-containing DNA sequences of living organisms are tested qualitatively and quantitatively. Extending previous studies, we demonstrate that these findings are trivially equivalent to variations of the base-pair composition in different regions of a DNA sequence. It is shown explicitly that a well-defined scaling or fractal exponent does not exist anywhere. Comparisons of natural DNAs with computer-generated, artificial sequences are made. The present study reveals that certain natural DNA sequences (especially those with compact genomes) do have stochastic characteristics which are intrinsically different from artificial sequences. The results for 21 DNA sequences of various types from widely different taxa are reported.

Variations in base pair composition and associated long-range correlations in DNA sequences--computer simulation results.

Recently, the possible occurrence of long-range correlations between nucleotides in DNA sequences of living organisms has excited considerable interest. Of particular importance is the claim that only intron-containing sequences exhibit these correlations. Different investigations, however, have disproved the claimed difference between intron-containing and intron-less DNA sequences. Moreover, very recent investigations pointed out that the long-range correlations appear only if relatively large variations in nucleotide composition along the DNA sequence are present. Furthermore, some examples demonstrated that these variations may have clear biological reasons. In this paper we investigate in detail, with the aid of computer simulations, the connection between compositional heterogeneity of a DNA sequence and the appearance of long-range correlations. As an explicit example, the DNA sequence of the lambda-phage is compared with different artificial sequences of similar compositional heterogeneity. The results demonstrate that the variations of the nucleotide composition along the sequence can fully account for all properties of the claimed long-range correlations. New results of extensive computer simulations are presented which clearly demonstrate how the apparent 'fractal' (or 'long-range-correlated') character of a sequence gradually evaporates, as the frequency of the compositional variations of a simulated sequence continuously increases.