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Comparative Study
. 2004 May;14(5):956-62.
doi: 10.1101/gr.1890304.

Sockeye: a 3D environment for comparative genomics

Stephen B Montgomery  1 , Tamara Astakhova, Mikhail Bilenky, Ewan Birney, Tony Fu, Maik Hassel, Craig Melsopp, Marcin Rak, A Gordon Robertson, Monica Sleumer, Asim S Siddiqui, Steven J M Jones
Affiliations
Comparative Study

Sockeye: a 3D environment for comparative genomics

Stephen B Montgomery et al. Genome Res. 2004 May.

Abstract

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.

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Figures

Figure 1
Figure 1
Multiple alignment visualization. Sockeye is simultaneously showing alignments for regions around the first exon of the Huntington's Disease gene (HD) from LAGAN (top four sequence tracks) and ClustalW (bottom four sequence tracks). The sequence tracks in order are (1) mouse, (2) rat, (3) human, (4) Fugu, (5) mouse, (6) rat, (7) human, and (8) Fugu. For the LAGAN algorithm, the start of translation of the HD gene in each species aligns perfectly. For the ClustalW algorithm, the start of translation for the first exon of the Fugu ortholog is misaligned. The Ensembl exon annotation includes the untranslated region. Ensembl-curated repeats are shown in red; gaps are shown in gray. This image shows how Sockeye can be used for comparative genomics and comparative algorithmics.
Figure 2
Figure 2
Sockeye GUI layout. (A) The menu. (B) The sequence track selection tree. From this component, a user can show/hide and obtain detailed information for loaded sequence tracks. (C) The feature selection tree. This component allows a user to show/hide annotation types. Its hierarchical structure is dynamically generated from Sockeye's XML start-up files. (D) The navigation toolbar. This component contains tools to navigate loaded sequence tracks. (E) The 3D viewport. This is where a user is able to perform analysis and visualization functions on 3D sequence tracks and annotations. (F) The status bar. This informs the user of the status of pending Ensembl queries and of memory usage.
Figure 3
Figure 3
Comparison of muscle specific regulatory modules in CACNL1AS/Cacna1s in human and mouse. Sockeye displays LRA predictions for muscle regulatory modules as a 3D grid, superimposed on genes (green exons, orange introns). Height and color intensity represent confidence that a specific region binds muscle-specific transcription factors. To obtain this image, we imported LRA score predictions as GFF and then created a distribution feature in Sockeye's import dialog.
Figure 4
Figure 4
SARS-CoV analysis. These sequence tracks show a BLASTX analysis of the SARS-CoV virus against (1) avian bronchitis virus, (2) bovine coronavirus, (3) human coronavirus 229E, (4) murine hepatitis, (5) porcine epidemic diarrhea virus, and (6) transmissible gastroenteritis virus. The last sequence track is SARS-CoV annotation imported from NCBI. This image shows dissimilarities between the SARS-CoV virus and other related viruses. These dissimilarities are pronounced in the structural proteins at the 3′ end (right). The score for each BLASTX hit is represented by height for each corresponding 3D feature in Sockeye. (Inset) The top view clearly shows the nature of the alignment.
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References

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WEB SITE REFERENCES

    1. http://www.bcgsc.bc.ca/sockeye; CMSGSC's Sockeye page.
    1. http://www.bcgsc.bc.ca/sockeye/gr2004_online_supplement; Sockeye version 1.0 User's Guide.
    1. http://www.bcgsc.ca/bioinfo/SARS/; CMSGSC SARS.
    1. db01.bcgsc.bc.ca; Ensembl data mirror.
    1. ensemb01.bcgsc.bc.ca:8082; Ensembl Web mirror.

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