A Stochastic Model for DNA Sequences Using Prescribed Nucleotide and Length Distributions

Author

Bergen, Stuart W A ; Antoniou, Andreas

Author_Institution

Dept. of Electr. & Comput. Eng., Victoria Univ., BC

fYear

2006

fDate

Aug. 2006

Firstpage

95

Lastpage

100

Abstract

A stochastic model that generates artificial DNA sequences with correlation characteristics similar to those observed in real DNA sequences is proposed. A Bernoulli-like process is used to generate patches of DNA with nucleotide content representative of coding and noncoding region. Alternating coding and noncoding DNA patches are concatenated to form the sequence where the patch length is based on sample statistics. Examples demonstrate that the nonuniform use of codons in coding regions is responsible for the often-observed period-three property. The amplitude of the correlation corresponding to the period-three property is proportional to the coding-region length and inversely proportional to the noncoding-region length. The correlation characteristics of the complete M.tuberculosis, B.subtilis, and S.cerevisiae (chromosome XI) genomes exhibit two distinct branches corresponding to period three and nonperiod-three correlations like those observed for the artificial DNA sequences

Keywords

DNA; genetics; stochastic processes; B.subtilis genome; Bernoulli-like process; DNA patches; M.tuberculosis genome; S.cerevisiae genome; artificial DNA sequences; chromosome XI genome; correlation characteristics; length distribution; noncoding region; nucleotide content representative; nucleotide distribution; period-three property; sample statistics; stochastic model; Autocorrelation; Bioinformatics; Biological cells; Character generation; DNA; Genomics; Information technology; Sequences; Signal processing; Stochastic processes; DNA modeling; Genomic DSP; period-three property;

fLanguage

English

Publisher

ieee

Conference_Titel

Signal Processing and Information Technology, 2006 IEEE International Symposium on

Conference_Location

Vancouver, BC

Print_ISBN

0-7803-9753-3

Electronic_ISBN

0-7803-9754-1

Type

conf

DOI

10.1109/ISSPIT.2006.270777

Filename

4042219