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DNAshapeR specifications

Information


Unique identifier OMICS_10994
Name DNAshapeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input data can be either nucleotide sequence(s) in FASTA file format or genomic intervals, provided by the user in BED format or derived from public databases.
Output data Minor groove width, helix twist, propeller twist and Roll can then be visualized in the form of plots, heat maps or genome browser tracks or used for the assembly of feature vectors of user-defined combinations of k-mer and shape features.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Remo Rohs

Publication for DNAshapeR

DNAshapeR citations

 (8)
library_books

Predicting double strand DNA breaks using epigenome marks or DNA at kilobase resolution

2018
Genome Biol
PMCID: 5856001
PMID: 29544533
DOI: 10.1186/s13059-018-1411-7

[…] ) and propeller twist (ProT) at base pair resolution and roll (Roll) and helix twist (HelT) at base pair step resolution using R package DNAshapeR (https://bioconductor.org/packages/release/bioc/html/DNAshapeR.html). […]

call_split

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

2018
PMCID: 5800008
PMID: 29409522
DOI: 10.1186/s13072-018-0174-4
call_split See protocol

[…] co-crystal structures (Additional file : Fig. S3). The methyl-DNAshape method is available as a web server at http://rohslab.usc.edu/methyl-DNAshape/ and as an extension to the R/Bioconductor package DNAshapeR [] at http://bioconductor.org/packages/devel/bioc/html/DNAshapeR.html. […]

call_split

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein induced DNA deformations

2018
Nucleic Acids Res
PMCID: 5946862
PMID: 29390080
DOI: 10.1093/nar/gky033
call_split See protocol

[…] d on the AMBER force field using collective and internal degrees of freedom in combination with implicit solvent, explicit sodium counter ions, and associated Jacobians (). The R/Bioconductor package DNAshapeR (), used for the prediction of minor groove width for naked DNA, is available at http://www.bioconductor.org/packages/devel/bioc/html/DNAshapeR.html. […]

library_books

Probing instructions for expression regulation in gene nucleotide compositions

2018
PLoS Comput Biol
PMCID: 5766238
PMID: 29293496
DOI: 10.1371/journal.pcbi.1005921

[…] insically linked to three-dimensional local structure of the DNA (DNA shape), we also computed, for each promoter segment (DU, CORE and DD), the mean scores of the four DNA shape features provided by DNAshapeR [] (helix twist, minor groove width, propeller twist, and Roll), adding 12 variables to the model. Although the difference between models with and without DNA shapes is also significant, the […]

library_books

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT content

2017
PLoS Genet
PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] To evaluate whether the local structure of the DNA has an effect on Hmga binding, we extended the mononucleotide model by incorporating structural information as predicted by the R package DNAshapeR []. DNAshapeR calculates for each pentamer in a given DNA sequence the minor groove width (MGW), the propeller twist (ProT), the helix twist (HelT) and the DNA roll (Roll), using values deri […]

library_books

Expanding the repertoire of DNA shape features for genome scale studies of transcription factor binding

2017
Nucleic Acids Res
PMCID: 5728407
PMID: 29165643
DOI: 10.1093/nar/gkx1145

[…] To make the additional DNA shape information broadly available, we extended our DNAshapeR package () built in R/Bioconductor. The software package is now not only able to predict the previously provided four shape features (MGW, Roll, ProT and HelT), but can also generate DNA sha […]

Citations

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DNAshapeR institution(s)
Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA, USA; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
DNAshapeR funding source(s)
This work was supported by the NIH (R01GM106056, R01HG003008 in part, and U01GM103804).

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