Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-Ro, Seongdong-Gu, Seoul, 133-791, Republic of Korea.
Genome Biol. 2023 Jul 17;24(1):170. doi: 10.1186/s13059-023-03009-5.
Structural variant (SV) calling belongs to the standard tools of modern bioinformatics for identifying and describing alterations in genomes. Initially, this work presents several complex genomic rearrangements that reveal conceptual ambiguities inherent to the representation via basic SV. We contextualize these ambiguities theoretically as well as practically and propose a graph-based approach for resolving them. For various yeast genomes, we practically compute adjacency matrices of our graph model and demonstrate that they provide highly accurate descriptions of one genome in terms of another. An open-source prototype implementation of our approach is available under the MIT license at https://github.com/ITBE-Lab/MA .
结构变异 (SV) 调用属于现代生物信息学的标准工具，用于识别和描述基因组中的改变。最初，这项工作提出了几种复杂的基因组重排，揭示了通过基本 SV 表示所固有的概念上的模糊性。我们从理论和实践上对这些模糊性进行了上下文分析，并提出了一种基于图的方法来解决它们。对于各种酵母基因组，我们实际计算了我们的图模型的邻接矩阵，并证明它们可以提供另一个基因组的高度准确描述。我们方法的开源原型实现可在 MIT 许可证下在 https://github.com/ITBE-Lab/MA 获得。
