Finding Borders between Coding and Noncoding DNA Regions by an Entropic Segmentation Method

Pedro Bernaola-Galván; Ivo Grosse; Pedro Carpena; José L. Oliver; Ramón Román-Roldán; H. Eugene Stanley

doi:10.1103/PhysRevLett.85.1342

Finding Borders between Coding and Noncoding DNA Regions by an Entropic Segmentation Method

Pedro Bernaola-Galván, Ivo Grosse, Pedro Carpena, José L. Oliver, Ramón Román-Roldán, and H. Eugene Stanley

Phys. Rev. Lett. 85, 1342 – Published 7 August 2000

Abstract

We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses only the general statistical properties of coding DNA. We find that this method is highly accurate in finding borders between coding and noncoding regions and requires no “prior training” on known data sets. Our results appear to be more accurate than those obtained with moving windows in the discrimination of coding from noncoding DNA.

Received 2 August 1999

DOI:https://doi.org/10.1103/PhysRevLett.85.1342

Authors & Affiliations

Pedro Bernaola-Galván^1,2,*, Ivo Grosse¹, Pedro Carpena^2,3, José L. Oliver⁴, Ramón Román-Roldán⁵, and H. Eugene Stanley¹

¹Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215
²Departamento de Física Aplicada II, Universidad de Málaga, E-29071, Spain
³Theoretical Physics, Oxford University, 1 Keble Road, OX1 3NP Oxford, England
⁴Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, E-18071, Spain
⁵Departamento de Física Aplicada, Universidad de Granada, E-18071, Spain