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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison
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SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison

机译：SEGA：基于结构的蛋白质比较的半全局图对齐

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摘要

Comparative analysis is a topic of utmost importance in structural bioinformatics. Recently, a structural counterpart to sequence alignment, called multiple graph alignment, was introduced as a tool for the comparison of protein structures in general and protein binding sites in particular. Using approximate graph matching techniques, this method enables the identification of approximately conserved patterns in functionally related structures. In this paper, we introduce a new method for computing graph alignments motivated by two problems of the original approach, a conceptual and a computational one. First, the existing approach is of limited usefulness for structures that only share common substructures. Second, the goal to find a globally optimal alignment leads to an optimization problem that is computationally intractable. To overcome these disadvantages, we propose a semiglobal approach to graph alignment in analogy to semiglobal sequence alignment that combines the advantages of local and global graph matching.
机译：比较分析是结构生物信息学中最重要的主题。最近，引入了与序列比对的结构对应物，称为多图比对，作为比较一般蛋白质结构和特别是蛋白质结合位点的工具。使用近似图匹配技术，该方法可以识别功能相关结构中的近似保守模式。在本文中，我们介绍了一种用于计算图对齐的新方法，该方法是由原始方法的两个问题（概念方法和计算方法）引起的。首先，现有方法对仅共享公共子结构的结构的实用性有限。其次，寻找全局最优路线的目标导致了在计算上难以解决的优化问题。为了克服这些缺点，我们提出了一种类似于半全局序列比对的半全局图对齐方法，该方法结合了局部图和全局图匹配的优点。

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