Comparative genomics techniques are used in bioinformatics analyses to identify 
the structural and functional properties of DNA sequences. As the amount of 
available sequence data steadily increases, the ability to perform large-scale 
comparative analyses has become increasingly relevant. In addition, the growing 
complexity of genomic feature annotation means that new approaches to genomic 
visualization need to be explored. We have developed a Java-based application 
called Sockeye that uses three-dimensional (3D) graphics technology to 
facilitate the visualization of annotation and conservation across multiple 
sequences. This software uses the Ensembl database project to import sequence 
and annotation information from several eukaryotic species. A user can 
additionally import their own custom sequence and annotation data. Individual 
annotation objects are displayed in Sockeye by using custom 3D models. 
Ensembl-derived and imported sequences can be analyzed by using a suite of 
multiple and pair-wise alignment algorithms. The results of these comparative 
analyses are also displayed in the 3D environment of Sockeye. By using the 
Java3D API to visualize genomic data in a 3D environment, we are able to 
compactly display cross-sequence comparisons. This provides the user with a 
novel platform for visualizing and comparing genomic feature organization.