RNA structural patterns

• Constraints:

  • string length
  • inter-string distance
  • character contents
  • matching positions
  • correlation (identical, reverse, complement).

• Complements a-u g-c, g-u (weaker)

• Structures: Stem-loops, Pseudo-knots, Clover leafs

• Context free grammar (stem loop), context sensitive grammar (pseudo-knots)

Eidhammer, Jonassen, Grinhang, Gilbert & Ratnayake, A contraint-based structure description language for biosequences, Journal of Constraints 6:2/3, 2001

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