Forest alignment with affine gaps and anchors, applied in RNA structure comparison
Forest alignment with affine gaps and anchors, applied in RNA structure comparison
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具有仿射间隙和锚点的森林对齐，应用于 RNA 结构比较
DOI：
10.1016/j.tcs.2012.07.040
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
R. Giegerich
中科院分区：
文献类型：
--
作者：
Stefanie Schirmer;R. Giegerich
我们提出了两个增强江的树比对算法，其用于RNA结构比对的经验的动机。一个改进是引入了仿射间隙模型，它可以适应于运行时间增加一个常数因子。第二个增强是当树中的某些节点通过所谓的锚定预对准时，对准算法的加速。这两个增强功能都包含在工具RNAforester的新实现中。我们评估了新算法与RNA二级结构分析相关的两个应用程序。根据我们的经验，我们提出了一个新的制定的树对齐模型，基于定期树语言和重写规则。
We present two enhancements to Jiang’s tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We evaluate the new algorithm with two applications related to RNA secondary structure analysis. Based on our experience, we suggest a new formulation of the tree alignment model, based on regular tree languages and rewrite rules.
影响因子：
14.9
作者：
Delcher, AL;Kasif, S;Salzberg, SL
通讯作者：
Salzberg, SL