RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2004 
FD May 01 
VO 14 
IS 5 
SP 956 
OP 962 
DO 10.1101/gr.1890304 
UL http://genome.cshlp.org/content/14/5/956.abstract 
AB 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.