Word organization in coding DNA: a mathematical model.
This article deals with the relationship between vocabulary (total number of distinct oligomers or "words") and text-length (total number of oligomers or "words") for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this relationship for CDSs. Here we develop a mathematical model to establish the relationship between the number of type of words (vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based on the parameters of the model, we formulate a mathematical equation, known as "equation of word organization", whose parameters essentially indicate that nucleotide organization of coding sequences are different from one another. We also compare the word organization of CDSs with the random word distribution and conclude that a CDS is neither similar to a natural human language nor to a random one. Moreover, these sequences have their unique nucleotide organization and it is completely structured for specific biological functioning.
Mukhopadhyay
Indranil
I
Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA-15261, USA. imukhopadhyay@hgen.pitt.edu
Som
Anup
A
Sahoo
Satyabrata
S
D001482:Base Composition; D001703:Biophysics / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry*; D005815:Genetic Code; D006801:Humans; D007802:Language; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D009711:Nucleotides / Q000737:chemistry
D009711:Nucleotides; D004247:DNA