Coding sequence density estimation via topological pressure

DOI10.1007/S00285-014-0754-2MaRDI QIDQ2512920zbMATH OpenOpenAlexWikidataFDO

Authors David Koslicki, Daniel J. Thompson

Publication date 2 February 2015

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1109.5999

coding sequence density estimation DNA sequence analysis topological pressure

Thermodynamic formalism, variational principles, equilibrium states for dynamical systems (37D35) Dynamical systems in biology (37N25) Computational methods for problems pertaining to biology (92-08) Protein sequences, DNA sequences (92D20)

Abstract: We give a new approach to coding sequence (CDS) density estimation in genomic analysis based on the topological pressure, which we develop from a well known concept in ergodic theory. Topological pressure measures the "weighted information content" of a finite word, and incorporates 64 parameters which can be interpreted as a choice of weight for each nucleotide triplet. We train the parameters so that the topological pressure fits the observed coding sequence density on the human genome, and use this to give ab initio predictions of CDS density over windows of size around 66,000bp on the genomes of Mus Musculus, Rhesus Macaque and Drososphilia Melanogaster. While the differences between these genomes are too great to expect that training on the human genome could predict, for example, the exact locations of genes, we demonstrate that our method gives reasonable estimates for the "coarse scale" problem of predicting CDS density. Inspired again by ergodic theory, the weightings of the nucleotide triplets obtained from our training procedure are used to define a probability distribution on finite sequences, which can be used to distinguish between intron and exon sequences from the human genome of lengths between 750bp and 5,000bp. At the end of the paper, we explain the theoretical underpinning for our approach, which is the theory of Thermodynamic Formalism from the dynamical systems literature. Mathematica and MATLAB implementations of our method are available at http://sourceforge.net/projects/topologicalpres/.

Review text

In this paper, the authors present a novel approach to genomic analysis using tools from the theory of thermodynamics. They adapt tools from thermodynamic formalism, particularly they adapt a well-known concept of ergodic theory and call it topological pressure. This feature is given by a weighted measure of complexity of a finite sequence. Two goals of the study were achieved: (1) using the topological pressure, applied on the human genome, it is predicted the coding sequence density on other genomes. This result gives a key practical advantage to the present approach, because it is possible to use only a single moderately phylogenetically distant informant genome as training data; (2) using the theory of thermodynamic formalism, the data encoded on the basis of topological pressure are turned into a probability distribution, which measures the coding potential of sequences of nucleotides of length between 750 and 5,000 bp. Another advantage of the present approach is its speed in calculation: the topological pressure can predict a coding sequence density for a genome in a matter of seconds, while ab initio prediction programs take a few hours, and evidence-based methods can take weeks.

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