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    • CAS: Chemistry: Scholarly Papers
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    •   OpenBU
    • College of Arts and Sciences
    • Chemistry
    • CAS: Chemistry: Scholarly Papers
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    GBshape: a genome browser database for DNA shape annotations

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    Nucl. Acids Re...pdf (2.107Mb)  Main article
    Chiu_etal_Supp...pdf (150.1Kb)  Supplementary data
    License
    Attribution 3.0 United States
    Date Issued
    2014-10-17
    Related DOI
    10.1093/nar/gku977
    Author
    Chiu, Tsu-Pei
    Yang, Lin
    Zhou, Tianyin
    Main, Bradley
    Parker, Stephen C.J.
    Nuzhdin, Sergey V.
    Tullius, Thomas D.
    Rohs, Remo
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    Permanent Link
    http://dx.doi.org/10.1093/nar/gku977
    https://hdl.handle.net/2144/9373
    Citation
    Chiu, Tsu-Pei, Yang, Lin, et al. "GBshape: a genome browser database for DNA shape annotations." Nucleic Acids Research, 17 October 2014. http://dx.doi.org/10.1093/nar/gku977
    Abstract
    Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.
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    Attribution 3.0 United States
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    • CAS: Chemistry: Scholarly Papers [49]

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