An Assessment of Prediction Algorithms for Nucleosome Positioning


Yoshiaki Tanaka[1][2] (ytanaka@hgc.jp)
Kenta Nakai[1][2][3] (knakai@ims.u-tokyo.ac.jp)

[1] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
[2] Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
[3] Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan

Abstract

Nucleosome configuration in eukaryotic genomes is an important clue to clarify the mechanisms of regulation for various nuclear events. In the past few years, numerous computational tools have been developed for the prediction of nucleosome positioning, but there is no third-party benchmark about their performance. Here we present a performance evaluation using genome-scale in vivo nucleosome maps of two vertebrates and three invertebrates. In our measurement, two recently updated versions of Segal's model and Gupta's SVM with the RBF kernel, which was not implemented originally, showed higher prediction accuracy although their performances differ significantly in the prediction of medaka fish and candida yeast. The cross-species prediction results using Gupta's SVM also suggested rather specific characters of nucleosomal DNAs in medaka and budding yeast. With the analyses for over- and under-representation of DNA oligomers, we found both general and species-specific motifs in nucleosomal and linker DNAs. The oligomers commonly enriched in all five eukaryotes were only CA/TG and AC/GT. Thus, to achieve relatively high performance for a species, it is desirable to prepare the training data from the same species.

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Japanese Society for Bioinformatics