TY  - JOUR
A1  - Montgomery, Stephen B.
A1  - Astakhova, Tamara
A1  - Bilenky, Mikhail
A1  - Birney, Ewan
A1  - Fu, Tony
A1  - Hassel, Maik
A1  - Melsopp, Craig
A1  - Rak, Marcin
A1  - Robertson, A. Gordon
A1  - Sleumer, Monica
A1  - Siddiqui, Asim S.
A1  - Jones, Steven J.M.
T1  - Sockeye: A 3D Environment for Comparative Genomics
Y1  - 2004/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 956 
EP  - 962 
DO  - 10.1101/gr.1890304 
VL  - 14 
IS  - 5 
UR  - http://genome.cshlp.org/content/14/5/956.abstract 
N2  - 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. 
ER  -