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Alignments of biomolecular contact maps
Interface Focus ( IF 4.4 ) Pub Date : 2021-06-11 , DOI: 10.1098/rsfs.2020.0066
Peter F Stadler 1, 2, 3, 4, 5, 6
Affiliation  

Alignments of discrete objects can be constructed in a very general setting as super-objects from which the constituent objects are recovered by means of projections. Here, we focus on contact maps, i.e. undirected graphs with an ordered set of vertices. These serve as natural discretizations of RNA and protein structures. In the general case, the alignment problem for vertex-ordered graphs is NP-complete. In the special case of RNA secondary structures, i.e. crossing-free matchings, however, the alignments have a recursive structure. The alignment problem then can be solved by a variant of the Sankoff algorithm in polynomial time. Moreover, the tree or forest alignments of RNA secondary structure can be understood as the alignments of ordered edge sets.



中文翻译:

生物分子接触图的排列

离散对象的对齐可以在非常一般的设置中构建为超级对象,通过投影从超级对象中恢复组成对象。在这里,我们专注于接触图,即具有一组有序顶点的无向图。这些作为 RNA 和蛋白质结构的自然离散化。在一般情况下,顶点有序图的对齐问题是 NP 完全的。然而,在 RNA 二级结构的特殊情况下,即无交叉匹配,比对具有递归结构。然后可以通过多项式时间内的 Sankoff 算法的变体来解决对齐问题。此外,RNA二级结构的树或森林比对可以理解为有序边集的比对。

更新日期:2021-06-11
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