Background Motifs are regulatory elements that will activate or inhibit the expression of related genes when proteins (such as transcription factors, TFs) bind to them. Therefore, motif finding is important to understand the mechanisms of gene regulation. De novo discovery of regulatory elements, like transcription factor binding sites (TFBSs), has long been a major challenge to gain insight on mechanisms of gene regulation. Recent advances in experimental profiling of genome-wide signals such as histone modifications and DNase I hypersensitivity sites allow scientists to develop better computational methods to enhance motif discovery. However, existing methods for motif finding suffer from high false positive rates and slow speed, and it's difficult to evaluate the performance of these methods systematically. Result Here we present MOST+, a motif finder integrating genomic sequences and genome-wide signals such as intensity and shape features from histone modification marks and DNase I hypersensitivity sites, to improve the prediction accuracy. MOST+ can detect motifs from a large input sequence of about 100 Mbs within a few minutes. Systematic comparison method has been established and MOST+ has been compared with existing methods. Conclusion MOST+ is a fast and accurate de novo method for motif finding by integrating genomic sequence and experimental signals as clues.
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机译：背景图案是当蛋白质（例如转录因子，TFS）与它们所结合时激活或抑制相关基因的表达的调节元件。因此，主题发现对于了解基因调控机制非常重要。 De Novo发现监管要素，如转录因子结合网站（TFBS），长期以来一直是深入了解基因调控机制的主要挑战。基因组信号的实验分析的最新进展，如组蛋白修饰和DNA酶I超敏点位点允许科学家培养更好的计算方法来增强基序发现。然而，现有的主题发现方法患有高误率和速度慢，并且难以系统地评估这些方法的性能。结果在这里我们存在大多数+，一个基因组序列集成基因组序列和基因组的信号，例如来自组蛋白修饰标记和DNase I超敏点的强度和形状特征，以提高预测精度。大多数+可以在几分钟内从大约100 MBS的大输入序列中检测图案。已经建立了系统的比较方法，大多数+已与现有方法进行了比较。结论大多数+是一种通过将基因组序列和实验信号作为线索集成基因组序列和实验信号来快速准确的德诺伊族来源。
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