On comparing composition principles of long DNA sequences with those of random ones. (June 2019)

• Record Type: Journal Article
• Authors: Fimmel, Elena; Gumbel, Markus; Karpuzoglu, Ali; Petoukhov, Sergey
• Is Part Of: Bio systems. Volume 180(2019)
• Page Start: 101
• Page End: 108
• Publication Date: 2019-06
• Subjects: DNA -- Chargaff's parity rules -- Genetic information; Biological systems -- Periodicals; Biology -- Periodicals; Biology -- Periodicals; Evolution -- Periodicals; Biologie -- Périodiques; Évolution -- Périodiques; 570
• DOI: 10.1016/j.biosystems.2019.04.003
• Languages: English
• ISSNs: 0303-2647

Abstract

Highlights: Generalized Chargaff's second parity rule (CSPR) for n -plets is formulated. Generalized CSPR is empirically verified for n -plets with n = 1, 2, …, 50. Uniformly distributed subsequences do not differ from random sequences. Equal-sized partitions behave by far differently compared with random sequences. The notion of a "long DNA-sequence" is quantified. Abstract: The revelation of compositional principles of the organization of long DNA sequences is one of the crucial tasks in the study of biosystems. This paper is devoted to the analysis of compositional differences between real DNA sequences and Markov-like randomly generated similar sequences. We formulate, among other things, a generalization of Chargaff's second rule and verify it empirically on DNA sequences of five model organisms taken from Genbank. Moreover, we apply the same frequency analysis to simulated sequences. When comparing the afore mentioned – real and random – sequences, significant similarities, on the one hand, as well as essential differences between them, on the other hand, are revealed and described. The significance and possible origin of these differences, including those from the viewpoint of maximum informativeness of genetic texts, is discussed. Besides, the paper discusses the question of what is a "long" DNA sequence and quantifies the choice of length. More precisely, the standard deviations of relative frequencies of bases stabilize from the length of approximately 100 000 bases, whereas the deviations are about three times as large at the length of approximately 25 000 bases.