4D bioinformatics: a new look at the ribosome as an example.
We have adapted the Java Molecular Viewer (JMV) to virtual reality display environments, through a number of extensions to the Java 3D code. Phylogenetic information derived from multiple alignments (temporal information) can be overlaid onto molecule structures (spatial information). The number of sequences included in the underlying multiple alignment can be changed instantaneously, resulting in dynamical updates of the displayed information. JMV was also extended to handle an infinite number of objects (molecules) in the same display. The objects can be manipulated in six degrees of freedom simultaneously or independently. We have used the small subunit ribosomal RNA to demonstrate the system (http:// cave.ucalgary.ca), which can be used for any molecule with a resolved structure.
Quon
Gerald T
GT
University of Calgary, Faculty o Medicine, Sun Center of Excellence for Visual Genomics, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1.
Gordon
Paul
P
Sensen
Christoph W
CW
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020459:Genes, rRNA; D010802:Phylogeny; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment