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SequenceJuxtaposer: Fluid Navigation For Large-Scale
Sequence Comparison in Context
James Slack*, Kristian Hildebrand*†, Tamara Munzner*
and Katherine St.John¥
* University of British Columbia,
† Bauhaus University Weimar,
¥ City University of New York
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Overview
Introduction Previous Work Interaction Metaphor SequenceJuxtaposer Conclusion and Future Work
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Introduction
Sequence visualization tool Exploration and comparison
Accordion Drawing Stretch and shrink rubber sheet Borders tacked down
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Introduction Video
Zur Anzeige wird der QuickTime™ Dekompressor „MPEG-4 Video“
benötigt.
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Previous Work
Accordion Drawing TreeJuxtaposer [Munzner 03]
Sequence Browsers Ensembl [Hubbard 02], UCSC Genome Browser [Kent
02], NCBI [Wheeler 02]
MacClade [Maddison 92], VISTA [Mayor 02],phylo-VISTA [Shah 03]
Artemis [Rutherford 00], LalnView [Duret 96], BARD [Spell 03], PipMaker [Schwartz 00]
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Accordion Drawing
SequenceJuxtaposer guarantees 3 key properties Context Visibility Frame Rate
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Guaranteed Context
Focus+Context Combine overview and detail into single view More information visible simultaneously Avoid getting lost while exploring Major information visualization research theme
Navigation metaphor Rubber sheet with borders tacked down
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Guaranteed Visibility
Highlight marks always visible Never fall outside of current view window Never hidden by something in front Never vanish, even if smaller than one pixel
Requires efficient algorithms Explicitly checking all items too slow
Linear in number of pixels, not number of items Details in TreeJuxtaposer paper
[Munzner et al, Siggraph03]
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Guaranteed Frame Rate
Need realtime update Focus+Context interaction must be fluid 20-30 frames per second
Computer graphics challenge Progressive rendering
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SequenceJuxtaposer
Fluid comparison of multiple sequences Handles DNA and RNA sequence data Provides searching, difference calculation
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SequenceJuxtaposer Video
Zur Anzeige wird der QuickTime™ Dekompressor „MPEG-4 Video“
benötigt.
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Algorithm Complexity
Sublinear: Runtime algorithms
Linear: User-initiated actions
Subquadratic: Preprocessing algorithms
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Searching
Search for motifs Protein/Codon search Regular expressions
supported Results marked with
guaranteed visibility
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Differences
Explore differences between aligned pairs Slider controls difference threshold in realtime
Results marked with guaranteed visibility
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Interaction
Resizing Expand or contract rectangular areas Drag visible rubberband interactively
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Interaction
Animated transitions Grow and shrink groups Allow user to track visual landmarks
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Drawing
Very high information density Avoid overdrawing in compressed areas Progressive rendering
Draw for fixed time, check for user interaction Priority queue to draw items in order of current
onscreen size
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Drawing Video
Zur Anzeige wird der QuickTime™ Dekompressor „MPEG-4 Video“
benötigt.
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Results and Performance
Java prototype using OpenGL, GL4Java Memory for AD data structures
significant, but linear paper: 1.7 million base pairs current: 20 Mbp
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Conclusion
Accordion Drawing for sequences Powerful new information visualization technique
Guarantees Context for maintaing orientation Visibility of landmarks: searches, differences Frame rate for realtime response to interaction
Fluid exploration of big datasets
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Future Work
Performance Memory, speed
Annotation Editing Connecting trees and sequences Other data types
BACs (bacterial artificial chromosomes)
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Open Source
Freely available from http://olduvai.sourceforge.net
SequenceJuxtaposerolduvai.sf.net/sj
TreeJuxtaposerolduvai.sf.net/tj
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Acknowledgements
Collaboration David Hillis and lab members, UT-Austin
Discussions Wayne Maddison, David Haussler, Nina Amenta
Technical writing Ciáran Llachlan Leavitt
Funding NSF/DEB-0121651/0121682 German Academic Exchange Service