Parameters for structures containing wobble base pair, single mimsatch, tandem mismatches or internal loop


Subnode name Attributes attributes values
mismatch sequence crick's pair XX/XX
    YRR/RRY
    RYY/YYR
    YYR/RYY
    YRY/RYR
    RRY/YYR
  size X (number of nucleotides)
  type initiation
    first-non-canonical-pair
  loop 1x2
    1xn-n>2
    2x3
    others-non-2x2
    1x1
  closing G/C
    C/G
    U/A
    A/U
    not-G/C
closure type per-A/U
    per-G/U
asymetry    
penalty type G/G-adjacent-AA-or-nonCanonicalPyrimidine
    AG-GA-UU-adjacent-UU-CU-CC-AA
parameters sequence A/A
    G/G
    U/U

Computational Neurobiology 2009-08-24