Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw, 02-097, Poland.
Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, Warsaw, 02-097, Poland.
BMC Genomics. 2020 Apr 16;21(Suppl 2):274. doi: 10.1186/s12864-020-6610-4.
The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently.
This work focuses on providing a tool for discovering and visualizing the relationships between the sequences constituting a pan-genome. A new structure to represent such relationships - called affinity tree - is proposed. Each node of this tree has assigned a subset of genomes, as well as their homogeneity level and averaged consensus sequence. Moreover, subsets assigned to sibling nodes form a partition of the genomes assigned to their parent.
Functionality of affinity tree is demonstrated on simulated data and on the Ebola virus pan-genome. Furthermore, two software packages are provided: PangTreeBuild constructs affinity tree, while PangTreeVis presents its result.
泛基因组一词被用来命名共同分析或用作参考的基因组序列集合。随着基因组数据的不断增长，开发用于有效研究泛基因组的数据结构和算法的工作也在不断增加。
本工作重点提供一种用于发现和可视化构成泛基因组的序列之间关系的工具。为此提出了一种新的结构来表示这种关系，称为亲和树。该树的每个节点都分配了一组基因组以及它们的同质性水平和平均共识序列。此外，分配给兄弟节点的子集构成分配给其父节点的基因组的分区。
亲和树的功能在模拟数据和埃博拉病毒泛基因组上得到了验证。此外，还提供了两个软件包：PangTreeBuild 构建亲和树，而 PangTreeVis 则呈现其结果。
