可指标方正块图的线性时间构造
Linear Time Construction of Indexable Founder Block Graphs
摘要：
我们介绍了一个紧凑的泛基因组表示的基础上，最佳分割的概念，旨在重建创始人序列从多序列比对（MSA）。这样的建立者序列具有MSA的每一行是建立者的重组的特征。先前已经设计了几种线性时间动态规划算法来优化诱导创始者块的分割，所述创始者块然后可以连接成一组创始者序列。所有可能的连接顺序都可以表示为创始人方块图。我们观察到这样的图的一个关键属性：如果节点标签（创始人段）不重复在图的路径中，这样的图可以被索引为有效的字符串匹配。我们称这样的图为无重复段的创始人块图。给出了一个线性时间算法来构造一个给定MSA的无段重复的创始者块图。该算法结合了创始人分割算法（Cazaux et al. SPIRE 2019）和全功能双向Burrows-Wheeler指数（Belazzougui和Cunial，CPM 2019）的技术。我们推导出一个简洁的索引结构，以支持查询的任意长度的路径图。报道了SAR-CoV-2毒株MSA的实验。大小为$410\times 29811$的MSA在一分钟内被压缩成3900个节点和4440条边的无段重复的创始者块图。节点标签的最大长度和总长度分别为12和34968。图上的索引仅占用MSA大小的$3\%$。
英文摘要：
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA is a recombination of the founders. Several linear time dynamic programming algorithms have been previously devised to optimize segmentations that induce founder blocks that then can be concatenated into a set of founder sequences. All possible concatenation orders can be expressed as a founder block graph. We observe a key property of such graphs: if the node labels (founder segments) do not repeat in the paths of the graph, such graphs can be indexed for efficient string matching. We call such graphs segment repeat-free founder block graphs. We give a linear time algorithm to construct a segment repeat-free founder block graph given an MSA. The algorithm combines techniques from the founder segmentation algorithms (Cazaux et al. SPIRE 2019) and fully-functional bidirectional Burrows-Wheeler index (Belazzougui and Cunial, CPM 2019). We derive a succinct index structure to support queries of arbitrary length in the paths of the graph. Experiments on an MSA of SAR-CoV-2 strains are reported. An MSA of size $410\times 29811$ is compacted in one minute into a segment repeat-free founder block graph of 3900 nodes and 4440 edges. The maximum length and total length of node labels is 12 and 34968, respectively. The index on the graph takes only $3\%$ of the size of the MSA.
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