GBshape   
Genome Browser
Table Browser
FTP
DNAshape
TFBSshape
Rohs Lab
Contacts
  About GBshape

DNA shape analysis has been established in recent years as an approach that reveals protein-DNA binding specificity determinants beyond nucleotide sequence. GBshape provides DNA shape annotations of entire genomes. The database currently contains annotations for minor groove width (MGW), propeller twist (ProT), Roll, helix twist (HelT), and hydroxyl radical cleavage (ORChID2) for 94 organisms. Additional genomes can easily be added in the provided framework. GBshape contains two major tools, a Genome Browser and a Table Browser. The Genome Browser provides a graphical representation of DNA shape annotations along standard genome browser annotations (Figure). The Table Browser enables the data manipulation, downloads, and basic statistical analyses. The DNA shape annotations were derived with a high-throughput method for DNA shape predictions (DNAshape) and constitute the whole-genome complement to a motif database of transcription factor binding sites (TFBSshape).

** Please cite any data retrieved from this web server as:
T.P. Chiu, L. Yang, T. Zhou, B.J. Main, S.C. Parker, S.V. Nuzhdin, T.D. Tullius, R. Rohs: GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res. 43, D103-109 (2015)






  News




April 3 2016

DNA shape annotions of Helicobacter pylori 26695 and Mycobacterium tuberculosis are added.


Nov. 23 2015

DNA shape annotions of Homo sapiens hg38 is added.


July 2 2015

DNA shape annotions of Caulobacter crescentus, Yarrowia lipolytica and Bacillus subtilis 168 are added.


Dec. 8 2014

FTP service is added. To download whole genome DNA shape data, please visit ftp://rohslab.usc.edu/


Oct. 10 2014

DNA shape annotions of Arabidopsis thaliana, Escherichia coli K12 and Plasmodium falciparum are added.


Sep. 15 2014

GBshape is functional and contains DNA shape annotations for 91 genomes.