TADBD: a sensitive and fast method for detection of typologically associated domain boundaries
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 computatio...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2020-07-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/btn-2019-0165 |
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| author | Hongqiang Lyu Lin Li Zhifang Wu Tian Wang Jiguang Zheng Hongda Wang |
| author_facet | Hongqiang Lyu Lin Li Zhifang Wu Tian Wang Jiguang Zheng Hongda Wang |
| author_sort | Hongqiang Lyu |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d18bdbce231c4cf4bf18ab507365c477 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2020-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-d18bdbce231c4cf4bf18ab507365c4772025-08-20T02:25:36ZengTaylor & Francis GroupBioTechniques0736-62051940-98182020-07-01691182510.2144/btn-2019-0165TADBD: a sensitive and fast method for detection of typologically associated domain boundariesHongqiang Lyu0Lin Li1Zhifang Wu2Tian Wang3Jiguang Zheng4Hongda Wang51School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China1School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China1School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China1School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China1School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China1School of Electronic & Information Engineering, Xi’an Jiaotong University, Xi’an 710049, ChinaA 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.https://www.future-science.com/doi/10.2144/btn-2019-0165haar-based algorithmHi-Ctopologically associated boundary detection |
| spellingShingle | Hongqiang Lyu Lin Li Zhifang Wu Tian Wang Jiguang Zheng Hongda Wang TADBD: a sensitive and fast method for detection of typologically associated domain boundaries BioTechniques haar-based algorithm Hi-C topologically associated boundary detection |
| title | TADBD: a sensitive and fast method for detection of typologically associated domain boundaries |
| title_full | TADBD: a sensitive and fast method for detection of typologically associated domain boundaries |
| title_fullStr | TADBD: a sensitive and fast method for detection of typologically associated domain boundaries |
| title_full_unstemmed | TADBD: a sensitive and fast method for detection of typologically associated domain boundaries |
| title_short | TADBD: a sensitive and fast method for detection of typologically associated domain boundaries |
| title_sort | tadbd a sensitive and fast method for detection of typologically associated domain boundaries |
| topic | haar-based algorithm Hi-C topologically associated boundary detection |
| url | https://www.future-science.com/doi/10.2144/btn-2019-0165 |
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