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- Title
Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.
- Authors
He, Xin; Huang, Xianhui; Long, Yuexuan; Liu, Zhenping; Chang, Xing; Zhang, Xianlong; Wang, Maojun
- Abstract
Summary TAD boundaries are essential for organizing the chromatin spatial structure and regulating gene expression in eukaryotes. However, for large-scale pan-3D genome research, identifying conserved and specific TAD boundaries across different species or individuals is computationally challenging. Here, we present Tcbf, a rapid and powerful Python/R tool that integrates gene synteny blocks and homologous sequences to automatically detect conserved and specific TAD boundaries among multiple species, which can efficiently analyze huge genome datasets, greatly reduce the computational burden and enable pan-3D genome research. Availability and implementation Tcbf is implemented by Python/R and is available at https://github.com/TcbfGroup/Tcbf under the MIT license.
- Subjects
MASSACHUSETTS Institute of Technology; GENOMICS; GENOMES; GENE expression; COMPARATIVE genomics; PYTHONS; CHROMATIN
- Publication
Bioinformatics, 2023, Vol 39, Issue 9, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btad576