Investigating some attributes of periodicity in DNA sequences via semi-Markov modelling

DOI10.1007/978-3-031-17820-7_9MaRDI QIDQ6153211zbMATH OpenOpenAlexFDO

Authors Pavlos Kolias, Alexandra Papadopoulou

Publication date 16 March 2024

Published in Springer Proceedings in Mathematics & Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1907.03119

zbMATH Keywords

DNA sequencepartial non-homogeneityquasiperiodicitysemi-Markov chains

Mathematics Subject Classification ID

Markov renewal processes, semi-Markov processes (60K15) Protein sequences, DNA sequences (92D20)

Abstract: DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies have used different methods, such as Fourier analysis and hidden-Markov models, in order to be able to predict which parts of a gene correspond to a protein encoding area. In this paper, a semi-Markov model is applied to 3-base periodic sequences, which characterize the protein-coding regions of the gene. Analytic forms of the related probabilities and the corresponding indexes are provided, which yield a description of the underlying periodic pattern. Last, the previous theoretical results are illustrated with DNA sequences of synthetic and real data.

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Cites work

• Applied Semi-Markov Processes
• Fitting Markov Chain Models to Discrete State Series such as DNA Sequences
• scientific article; zbMATH DE number 1260708 (Why is no real title available?)
• scientific article; zbMATH DE number 699389 (Why is no real title available?)
• scientific article; zbMATH DE number 4116364 (Why is no real title available?)
• scientific article; zbMATH DE number 1447424 (Why is no real title available?)
• scientific article; zbMATH DE number 3361677 (Why is no real title available?)
• Non-homogeneous semi-Markov systems and maintainability of the state sizes
• On the spectral criteria of disorder in nonperiodic sequences: application to inflation models, symbolic dynamics and DNA sequences
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
• Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence
• Some results on modeling biological sequences and web navigation with a semi Markov chain
• Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition

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