Biomedical Engineering Reference
In-Depth Information
The difference between the experimental and predicted structures in (A) is uniformly distributed.
However, in (B), most of the molecules match exactly. The single point of deviation is responsible for
the majority of the RMSD score. In (C), there is considerable mismatch in structure, but because of
the small number of atoms involved in the calculation, the RMSD score seems to indicate a good
match. For example, even though the larger molecules in (D) have the same RMSD score, the
overlap is much tighter along the entire length of the proteins.
Regardless of the visualization technologies used, the underlying assumption is that, for most
researchers, the perceptual clues in graphical displays can enhance immediate understanding of the
data being presented. Visualization technologies can provide an intuitive representation of the
relationships among large groups of objects or data points that could otherwise be incomprehensible,
while providing context and indications of relative importance.
This chapter explores data visualization techniques applicable to bioinformatics, from methods of
generating 3D renderings of protein structures to creating maps of the physical location of genes on
the chromosomes. The "
Sequence Visualization
" and "
Structure Visualization
" sections explore the
technologies available to help researchers visualize nucleotide sequence data and protein structure
data, respectively. The remainder of the chapter deals with the underlying technologies. For example,
the "
User Interface
" section looks at how visualization techniques can make bioinformatics
applications more easily understood and learned. "Animation Versus Simulation" explores difference
between the two technologies, as applied to visualization. The "
General Purpose
" section explores the
use of general-purpose software and hardware technologies that can be applied to bioinformatics.
The "
On the Horizon
" and "
Endnote
" sections consider the prospects of practical virtual reality and
other near-future visualization technologies.
