核小体定位预测算法的评估。

Yoshiaki Tanaka, K. Nakai
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引用次数: 16

摘要

真核生物基因组中的核小体结构是阐明各种核事件调控机制的重要线索。在过去的几年中,已经开发了许多用于预测核小体定位的计算工具,但是没有第三方基准来衡量它们的性能。在这里,我们提出了一个性能评估使用基因组规模的核小体在体内两种脊椎动物和三种无脊椎动物。在我们的测量中,两个最近更新版本的Segal模型和Gupta的支持向量机与RBF内核(最初没有实现),显示出更高的预测精度,尽管它们在预测medaka鱼和念珠菌方面的性能差异很大。Gupta支持向量机的跨种预测结果也显示了medaka和出芽酵母核小体dna的特异性。通过分析DNA低聚物的代表性和代表性不足,我们在核小体和连接体DNA中发现了一般和物种特异性基序。5种真核生物中普遍富集的低聚物只有CA/TG和AC/GT。因此,为了获得一个物种相对较高的性能,需要准备来自同一物种的训练数据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
An assessment of prediction algorithms for nucleosome positioning.
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-representat ion 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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