An Evolutionary Model of DNA Substring Distribution
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DNA sequence analysis methods, such as motif discovery, gene detection or phylogeny reconstruction, can often provide important input for biological studies. Many of such methods require a background model, representing the expected distribution of short substrings in a given DNA region. Most current techniques for modeling this distribution disregard the evolutionary processes underlying DNA formation. We propose a novel approach for modeling DNA k-mer distribution that is capable of taking the notions of evolution and natural selection into account. We derive a computionally tractable approximation for estimating k-mer probabilities at genetic equilibrium, given a description of evolutionary processes in terms of fitness and mutation probabilities. We assess the goodness of this approximation via numerical experiments. Besides providing a generative model for DNA sequences, our method has further applications in motif discovery.
KeywordsBackground Model Motif Discovery Transcription Factor Binding Motif Genetic Equilibrium Inductive Bias
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- 1.Davidson, E.H.: The regulatory genome: gene regulatory networks in development and evolution. Academic Press, San Diego (2006)Google Scholar
- 8.Brazma, A., Jonassen, I., Vilo, J., Ukkonen, E.: Predicting gene regulatory elements in silico on a genomic scale. Genome. Res. 8(11), 1202–1215 (1998)Google Scholar
- 11.Vilo, J.: Pattern discovery from biosequences. Thesis PhD (2002)Google Scholar
- 14.Varadarajan, A., Bradley, R., Holmes, I.: Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome. Biol. 9(10), R147 (2008)Google Scholar