On the representability of complete genomes by multiple competing finite-context (Markov) models

• Published in: PloS one Vol. 6; no. 6; p. e21588
• Main Authors: Pinho, Armando J, Ferreira, Paulo J S G, Neves, António J R, Bastos, Carlos A C
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30-06-2011; Public Library of Science (PLoS)
• Subjects: Animals; Biology; Compression; Computational Biology - methods; Data compression; Deoxyribonucleic acid; DNA; DNA sequencing; Engineering; Entropy; Estimates; Eukaryotes; Gene sequencing; Genome - genetics; Genomes; Genomics; Humans; Information theory; Inverted repeat; Markov Chains; Markov processes; Mathematical models; Mathematics; Methods; Nucleotide sequence; Position measurement; Probability distribution; Probability distributions; Prokaryotes; Proteins; Signal processing; Social and Behavioral Sciences; Statistical analysis; Statistical models; Portugal
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0021588

A finite-context (Markov) model of order k yields the probability distribution of the next symbol in a sequence of symbols, given the recent past up to depth k. Markov modeling has long been applied to DNA sequences, for example to find gene-coding regions. With the first studies came the discovery that DNA sequences are non-stationary: distinct regions require distinct model orders. Since then, Markov and hidden Markov models have been extensively used to describe the gene structure of prokaryotes and eukaryotes. However, to our knowledge, a comprehensive study about the potential of Markov models to describe complete genomes is still lacking. We address this gap in this paper. Our approach relies on (i) multiple competing Markov models of different orders (ii) careful programming techniques that allow orders as large as sixteen (iii) adequate inverted repeat handling (iv) probability estimates suited to the wide range of context depths used. To measure how well a model fits the data at a particular position in the sequence we use the negative logarithm of the probability estimate at that position. The measure yields information profiles of the sequence, which are of independent interest. The average over the entire sequence, which amounts to the average number of bits per base needed to describe the sequence, is used as a global performance measure. Our main conclusion is that, from the probabilistic or information theoretic point of view and according to this performance measure, multiple competing Markov models explain entire genomes almost as well or even better than state-of-the-art DNA compression methods, such as XM, which rely on very different statistical models. This is surprising, because Markov models are local (short-range), contrasting with the statistical models underlying other methods, where the extensive data repetitions in DNA sequences is explored, and therefore have a non-local character.