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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability
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Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability

机译：利用DNA热力学稳定性快速预测DNA熔解气泡

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摘要

DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu
机译：DNA融化气泡是许多DNA与蛋白质相互作用的基础，例如驱动基因表达，DNA复制和细菌水平基因转移的调节性DNA区域中的相互作用。气泡形成受到DNA双链体稳定性和热诱导双链体不稳定（TIDD）的影响。尽管使用最近邻（NN）方法预测双链体稳定性要比使用Peyrard-Bishop-Dauxois（PBD）模型预测TIDD快得多，但是PBD预测TIDD定义了具有更高准确度和详细度的调节DNA区域。在这里，我们认为PBD预测的TIDD与去稳定化区域的固有双链体稳定性内在相关。我们通过回归模型表明，NN双工稳定性可用于预测TIDD，几乎与PBD一样准确。预测的TIDD实际上归因于不稳定区域中NN双工稳定性的非线性变换以及相对于不稳定大小的邻近区域的影响。由于我们模型的预测时间比PBD的预测时间短了六个数量级，因此模型为研究人员提供了可访问的工具。可以在我们的Web服务器上（http://tidd.immt.eu）预测TIDD

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