Computer prediction of sites associated with various elements of the nuclear matrix.
Computer prediction of sites associated with various elements of the nuclear matrix.
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DOI：
10.1093/bib/1.1.33
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发表时间：
2000-02-01
影响因子：
9.5
通讯作者：
Glazkov, M V
中科院分区：
文献类型：
--
作者：
Rogozin, I B;Glazko, G V;Glazkov, M V
真核细胞染色体DNA与核骨架/基质的连接区（S/MAR）参与各种重要的细胞过程。然而，没有明显的特征，这些核苷酸序列已被揭示，除了S/MAR的非编码位点含有推定的调控元件和DNA-拓扑异构酶II的结合位点。S/MARs之间的异质性可能是由多种生物因素引起的。本文比较了两种S/MARs预测程序MAR-CLASS（Singh，克雷默and Krawetz，1997）和ChrClass（Glazkov，Rogozin and Glazko，1998）的准确性，认为这两种程序均可推荐用于真核生物基因组分析。然而，他们的预测结果应谨慎解释，因为这两个程序的预测精度的估计需要进一步的分析。S/MARs预测的问题上的几个例子说明人类蛋白质编码基因，重复元件和β-珠蛋白基因座从不同的哺乳动物物种。我们的分析结果表明，ChrClass错过S/MAR的比例较低，而MAR-MARS（默认参数集）错误S/MAR的比例较低。
Attachment regions of the eukaryotic chromosomal DNA to the nuclear scaffold/matrix (S/MARs) participate in various important cellular processes. However, no obvious characteristics common for these nucleotide sequences have been revealed, except that S/MARs are non-coding sites containing putative regulatory elements and binding sites of DNA-topoisomerase II. Heterogeneity among S/MARs can be caused by a variety of biological factors. In this paper, the accuracy of two S/MARs prediction programs, MAR-Finder (Singh, Kramer and Krawetz, 1997) and ChrClass (Glazkov, Rogozin and Glazko, 1998) are compared and it is concluded that both programs can be recommended for analysis of eukaryotic genomes. However, results of their prediction should be interpreted with caution since estimation of prediction accuracy of both programs needs further analysis. Problems of S/MARs prediction are illustrated on several examples of human protein-coding genes, repeated elements and the beta-globin locus from different mammalian species. Results of our analysis suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder (a default set of parameters).