DNAshape statistics

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DNAshape specifications

Information


Unique identifier OMICS_09340
Name DNAshape
Interface Web user interface
Restrictions to use None
Input data DNA sequence(s)
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No

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This tool is not available anymore.

Publication for DNAshape

DNAshape in publications

 (18)
PMCID: 5840810
PMID: 29510689
DOI: 10.1186/s12859-018-2104-7

[…] –]. recently there have been several studies showing that variations in dna shape can influence tf binding affinity, and that those contributions may involve non-independence between positions [–]. dnashape is a program that predicts dna structural features in a high-throughput manner based on monte carlo simulations of dna fragments []. the genome browser for dna shape annotations (gbshape), […]

PMCID: 5822049
PMID: 29472273
DOI: 10.15252/msb.20177902

[…] have the same value in the table) were left out separately. linear regression on k‐mer tables is implemented in the program kmerlinearregression.py. the shape tables were generated by querying the dnashape webserver for all pentamer sequences (zhou et al, )., while the log‐likelihood of the nrlb model in principle measures how well a binding model fits the selex‐seq data, this value […]

PMCID: 5800008
PMID: 29409522
DOI: 10.1186/s13072-018-0174-4

[…] number of experimentally determined structures. to achieve a better mechanistic understanding of the effect of cpg methylation on local dna structure, we developed a high-throughput method, methyl-dnashape, for predicting the effect of cytosine methylation on dna shape., using our new method, we found that cpg methylation significantly altered local dna shape. four dna shape features—helix […]

PMCID: 5946862
PMID: 29390080
DOI: 10.1093/nar/gky033

[…] had the same structure as naked dna, and part changed structure upon protein binding. we compared the experimental map with minor groove patterns of dna predicted by two computational approaches, dnashape and orchid2, and found good but not perfect concordance with both. this experimental approach will be useful in mapping structures of dna sequences for which high-resolution structural data […]

PMCID: 5728407
PMID: 29165643
DOI: 10.1093/nar/gkx1145

[…] the mc data provided an average coverage of 249.8 for each unique tetramer. although the pdb contains additional dna structures, we used the original xrc dataset to be consistent with our original dnashape method (). xrc data were filtered for unusual deformations, and chemically modified structures were removed as previously described (). the different coverage of tetramers in the md, xrc […]


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DNAshape institution(s)
Molecular and Computational Biology Program, Department of Biological Sciences; Department of Physics and Astronomy; Department of Chemistry; Department of Computer Science; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA

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