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.

Contents

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
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