I'm trying to compare the output of 2 different algorithms of RNA structure prediction (my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA package.
I'm getting a distance score of 38 between Nussinov prediction and the actual NMR structure, and a score of 14 between the m-fold algorithm and the NMR structure and I'm trying to understand whether it is a big difference.
In order to do that I have to look at the scoring table that is used by RNAdistance and found the following score table in the source code:
RIVATE CostMatrix UsualCost =
{
/* Null, U, P, H, B, I, M, S, E, R */
{ 0, 1, 2, 2, 2, 2, 2, 1, 1, DIST_INF}, /* Null replaced */
{ 1, 0, 1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF}, /* U replaced */
{ 2, 1, 0, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF}, /* P replaced */
{ 2, DIST_INF, DIST_INF, 0, 2, 2, 2, DIST_INF, DIST_INF, DIST_INF}, /* H replaced */
{ 2, DIST_INF, DIST_INF, 2, 0, 1, 2, DIST_INF, DIST_INF, DIST_INF}, /* B replaced */
{ 2, DIST_INF, DIST_INF, 2, 1, 0, 2, DIST_INF, DIST_INF, DIST_INF}, /* I replaced */
{ 2, DIST_INF, DIST_INF, 2, 2, 2, 0, DIST_INF, DIST_INF, DIST_INF}, /* M replaced */
{ 1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, 0, DIST_INF, DIST_INF}, /* S replaced */
{ 1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, 0, DIST_INF}, /* E replaced */
{ DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, 0}, /* R replaced */
};
I also found the enter link description herefollowing explanation, but I do not understand what is the meaning of the table letters: U,P,H,B,I,MS,E,R ?
What is the meaning of the score of [H,B] = 2 for example?
If anyone can explain the table it will be a great help in my project, thank you!
Ok, the answer was right here and I missed it, posting it in case anyone else will do the same mistake as me in the future.
U = unpaired
P = paired
H = hairpin
B = bulge
I = internal loop
M = multiloop
S = stem (or stack)
E = external loop