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dc.contributor.authorChiu, Tsu-Peien_US
dc.contributor.authorYang, Linen_US
dc.contributor.authorZhou, Tianyinen_US
dc.contributor.authorMain, Bradleyen_US
dc.contributor.authorParker, Stephen C.J.en_US
dc.contributor.authorNuzhdin, Sergey V.en_US
dc.contributor.authorTullius, Thomas D.en_US
dc.contributor.authorRohs, Remoen_US
dc.date.accessioned2014-10-24T17:54:25Z
dc.date.available2014-10-24T17:54:25Z
dc.date.issued2014-10-17
dc.identifier.citationChiu, 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
dc.identifier.urihttp://dx.doi.org/10.1093/nar/gku977
dc.identifier.urihttps://hdl.handle.net/2144/9373
dc.description.abstractMany 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.en_US
dc.description.sponsorshipNational Institutes of Health (R01GM106056, U01GM103804, R01HG003008); Alfred P. Sloan Foundation; National Science Foundation (MCB-1413539).en_US
dc.language.isoen
dc.publisherOxford University Pressen_US
dc.rightsAttribution 3.0 United Statesen_US
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/
dc.subjectGenome structureen_US
dc.subjectDNA shapeen_US
dc.subjectNucleosome positioningen_US
dc.subjectTranscription start siteen_US
dc.subjectProtein-DNA recognitionen_US
dc.titleGBshape: a genome browser database for DNA shape annotationsen_US
dc.typeArticleen_US
dc.identifier.doi10.1093/nar/gku977


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Attribution 3.0 United States
Except where otherwise noted, this item's license is described as Attribution 3.0 United States