School of Electronic & Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
School of Automation Science & Electrical Engineering, Beihang University, Beijing 100191, China.
Biotechniques. 2020 Jul;69(1):376-383. doi: 10.2144/btn-2019-0165. Epub 2020 Apr 7.
A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. This method implements a Haar-based algorithm by considering Haar diagonal template, acceleration via a compact integrogram, multi-scale aggregation at template size and statistical filtering. In most cases, comparison results from simulated and experimental data show that TADBD outperforms the other five methods. In addition, a new R package for TADBD is freely available online.
拓扑关联域 (TAD) 是一个自我相互作用的基因组块。在 TAD 水平上分析 3D 基因组结构时，检测 Hi-C 接触矩阵上的 TAD 边界是最重要的问题之一。在这里，我们提出了 TAD 边界检测 (TADBD)，这是一种用于在 Hi-C 接触矩阵上检测 TAD 边界的敏感且快速的计算方法。该方法通过考虑 Haar 对角模板、紧凑积分图的加速、模板大小的多尺度聚合和统计滤波来实现基于 Haar 的算法。在大多数情况下，来自模拟和实验数据的比较结果表明 TADBD 优于其他五种方法。此外，一个用于 TADBD 的新 R 包可在线免费获得。
