Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37725346.
- Also identified by DOI 10.1093/bioinformatics/btad576 and PMC identifier 10539074.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. Tcbf is implemented by Python/R and is available at https://github.com/TcbfGroup/Tcbf under the MIT license.
Medical subject headings
- Software
- Genome