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.