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Sequence Visualization for Genomic DNA
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Analysis and Visualizations Using GENVIS
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We developed a software platform in which large DNA sequence datasets may
be visualized by techniques which readily reveal patterns and insights.
Initially we focused on providing accurate statistical visualizations rather
than quantitative presentations. An example application of this platform
visualizes properties of DNA sequence strings of any size as a function of
string position (for example, in large chromosome).
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Figure 1.
DNA Sequence Properties Displayed as a Function of the Sequence Position
Display of the output of GENVIS, a platform that calculates properties of
DNA sequences in a moving window along the sequence, as a function of the
sequence position. The sequence presented is a 33 kb region from S.
cereviseae. For the sequence TGGT, the function calculated is the % difference
between the observed frequency of TGGT in the moving window and the expected
frequency of TGGT in that window calculated from the window base composition.
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Figure 2.
Display of Individual DNA Sequence Positions
Display of the color pixel coded individual base positions along a portion
of yeast chromosome III organized in a serpentine fashion vertically.
Reference base positions along the DNA sequence are shown on the vertical
axis.
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LINK 1:
"GENVIS", published in Proceedings of SPIE Volume 2656, 1996.
(Off site link)
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