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TopDom specifications

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Unique identifier OMICS_16876
Name TopDom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A Hi-C contact map.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.0.2
Stability Stable
Maintained Yes

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Publication for TopDom

TopDom citations

 (8)
library_books

High resolution TADs reveal DNA sequences underlying genome organization in flies

2018
Nat Commun
PMCID: 5768762
PMID: 29335486
DOI: 10.1038/s41467-017-02525-w

[…] low coverage bins is 570 bp. for the 6-cutter hindiii the average was 4500 bp., tad boundaries were identified using an improved version of tad-separation score method from ref. which is similar to topdom. the method works by first transforming the hi-c contact matrix into a z-score matrix a\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} […]

library_books

TAD free analysis of architectural proteins and insulators

2017
Nucleic Acids Res
PMCID: 5861416
PMID: 29272504
DOI: 10.1093/nar/gkx1246

[…] on the tad algorithm used in drosophila (figure ). for instance, gaf presented an odds ratio (or) of 4.3 with hicseg (), an or of 4 with arrowhead (), whereas it only showed an or of 2.5 with topdom tads (). conversely, dctcf presented an or of 3.7 with hicseg, and ors around 5 with arrowhead and topdom., instead of testing protein enrichments at tad borders, we used our model to directly […]

library_books

Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

2017
Genes
PMCID: 5615356
PMID: 28885554
DOI: 10.3390/genes8090223

[…] and the conserved chromatin organization []. to infer the hierarchy of the nested structure, tadtree was recently introduced based on empirical distributions of contact frequencies within tads []. topdom is another easy-to-implement pipeline to study cross-tissue tad conservation []. to tackle terabase-size data for those with less informatics experience, juicer is recommended as a one-click […]

library_books

Condensin mediated remodeling of the mitotic chromatin landscape in fission yeast

2017
Nat Genet
PMCID: 5621628
PMID: 28825727
DOI: 10.1038/ng.3938

[…] with those observed in interphase, suggesting that interphase tads fuse to give rise to larger chromosome domains in mitosis. we reached the same conclusions when we used an alternative algorithm, (topdom), to assign domain boundaries ()., we started to address how condensin promotes longer-range interactions by performing chip to determine condensin binding sites. we divided the chromosome […]

library_books

A critical assessment of topologically associating domain prediction tools

2017
Nucleic Acids Res
PMCID: 5389712
PMID: 28334773
DOI: 10.1093/nar/gkx145

[…] each condition; gamma was tested from 0.005 to 1 at increments of 0.005 with s = 0.005. the value of gamma that produced tads closest to the number of tads predicted by other tools was used (see ). topdom produced tad annotations that divide genomic regions to ‘domain’, ‘boundaries’ and ‘gaps’. to compare with other tools, only regions labeled ‘domain’ were used in this analysis. tadtree […]

library_books

The human transmembrane proteome

2015
Biol Direct
PMCID: 4445273
PMID: 26018427
DOI: 10.1186/s13062-015-0061-x

[…] the topology information and may be used in the same manner as the results of topology experiments. such a combination of domain/motif data with topology data were used during the creation of the topdom database [] by a fully automated algorithm. it was also shown, by identifying a set of 367 domains from soluble proteins in the smart database which have compartment-specific localization […]


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TopDom institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA; Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
TopDom funding source(s)
Supported by National Institutes of Health (NIH) [NHLBI MAPGEN U01HL108634, U54 DK107981]; NSF [CAREER 0747475, CAREER 1150287]; Arnold and Mabel Beckman foundation [BYI award]; Pew Charitable Trusts [Pew Scholarship].

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