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