VMM: A Variable Memory Markov Model Prediction of Nucleosome Formation Sites

Abstract

Prediction of the DNA capacity to form nucleosome structure based on sequence statistics is of importance in analysis of gene expression regulation in eukaryotes. Context analysis of nucleotide sequences of experimentally defined nucleosome formation sites allows the determination of the sequence preference for nucleosome formation relying on statistical information. However, context analysis does not allow identifying the clear-cut consensus making feasible site prediction. One has to make recourse to more general context sequence features, such as dinucleotide frequencies. Markov model is a common approach to the prediction of the functional regions in DNA sequences that disregards positional information. Here, we use an improved version of the Markov model to predict the preference of DNA sequences to be within a nucleosome structure. The developed VMM program (the Variable Memory Markov model) computes the nucleosome formation potential for genomic DNA sequences of arbitrary lengths, including the short transcription factor binding sites. The VMM is publicly available at <http://wwwmgs.bionet.nsc.ru/programs/VMM/>.