Biogang:Projects/Visualization of biological data

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This is supposed to be a book or a longer document describing current approaches of data visualization.

Proteins

Types of data

• sequence
• structure
• interactions and other networks
• dynamics
• folding

Visualization of sequence data

• sequence itself
• similarities: dotplot
• multidimensional sequence data: sequence logo, profile or HMM
• secondary structure mapped onto sequence
• spectrum, statistics, Fourier transform
• regular expressions
• binary schemas
• melody

Visualization of structural data

• water accessible surface, colors according to physical properties, sequence conservartion etc.
• structural elements: ss, sse, domains, cartoons
• activity
• electrostatics
• connections, internal coordinates, contact maps
• density maps