SequenceJuxtaposer: Fluid Navigation For Large-Scale Sequence Comparison In Context

SequenceJuxtaposer: Fluid Navigation For Large-Scale Sequence Comparison In Context

James Slack, Kristian Hildebrand, Tamara Munzner, and Katherine St. John
Proc. German Conference on Bioinformatics 2004, pp 37-42

PDF | Abstract | Videos | Software | Figures | Talk

Paper

final PDF (5 pages)
submitted PDF (12 pages)

Abstract

SequenceJuxtaposer is a sequence visualization tool for the exploration and comparison of biomolecular sequences. We use an information visualization technique called ``accordion drawing'' that guarantees three key properties: context, visibility, and frame rate. We provide context through the navigation metaphor of a rubber sheet that can be smoothly stretched to show more details in the areas of focus, while the surrounding regions of context are correspondingly shrunk. Landmarks, such as user specified motifs or differences between aligned base pairs across multiple sequences, are guaranteed to be visible even if located in the shrunken areas of context. Our graphics infrastructure for progressive rendering provides immediate responsiveness to user interaction by guaranteeing that we redraw the scene at a target frame rate. Our preprocessing algorithms are subquadratic: O(nk) for k sequences of n base pairs each. All runtime rendering algorithms are sublinear in nk: they are O(v) where v is the number of items visible onscreen at once, and v \ll nk. SequenceJuxtaposer supports interaction at 20 frames per second when browsing collections of several hundred sequences that comprise over 1.7 million total base pairs. We show three example applications with large, publicly available datasets, and we are able to quickly observe many features that had previously required significant analysis to discover.

Videos

QuickTime videos include voiceover

introduction [13MB]
OY motif search, zoom (Fig 1 in action) [4 MB]
CNR1 difference thresholds (Fig 3 in action) [11MB]
high-resolution display [38MB]

Software

Download page

Figures

Figure 1: OY genome (680 Kbp) zoom after motif search
Figure 2: OY TMK gene motifs: P-loop top, TMP binding below
Figure 3: CNR1 gene from 44-mammal Murphy dataset, at 4 different difference thresholds
Figure 4: treezilla dataset (500 seed-plant rbcL sequences of 1428 bp each, 714 Kbp total) showing codon bias

Talk

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Last modified: Tue Jul 1 17:04:44 PDT 2008