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Bioinformatics. 2018 Apr 15;34(8):1409-1410. doi: 10.1093/bioinformatics/btx805.

Delta: a new web-based 3D genome visualization and analysis platform.

Tang B1,2,3, Li F1, Li J1, Zhao W2, Zhang Z1,3.

Author information

1
CAS Key Laboratory of Genome Sciences and Information, Chinese Academy of Sciences, Beijing 101300, China.
2
BIG Data Center (BIGD), Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.
3
University of Chinese Academy of Sciences, Beijing 100049, China.

Abstract

Summary:

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. Finally, by visually comparing the 3D model of the β-globin gene locus and its annotation, we speculated a plausible transitory interaction pattern in the locus. Experimental evidence was found to support this speculation by literature survey. This served as an example of intuitive hypothesis testing with the help of Delta.

Availability and implementation:

Delta is freely accessible from http://delta.big.ac.cn, and the source code is available at https://github.com/zhangzhwlab/delta.

Contact:

zhangzhihua@big.ac.cn.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29253110
DOI:
10.1093/bioinformatics/btx805
[Indexed for MEDLINE]

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