生物信息学：了解 ViennaRNA RNAdistance 评分 table

Question

我正在尝试比较 2 种不同的 RNA 结构预测算法的输出（我的 Nussinov vs RNA-mfold 算法的实现）使用 RNAdistance algorithm that is part of ViennaRNA 包。

我得到 Nussinov 预测和实际 NMR 结构之间的距离得分为 38，m 倍算法和 NMR 结构之间的距离得分为 14，我正在尝试了解它是否是一个大的差异。

为了做到这一点，我必须查看 RNAdistance 使用的评分 table，并在 source code 中找到以下 score table：

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 */

};

我也找到了enter link description here下面的解释，但是我不明白table字母U,P,H,B,I, MS,E,R ?

比如分数[H,B] = 2是什么意思？

谁能解释一下table对我的项目会有很大的帮助，谢谢！

Answer 1

好的，答案是正确的here我错过了，张贴它以防其他人将来犯同样的错误。

U = unpaired
P = paired
H = hairpin
B = bulge
I = internal loop
M = multiloop
S = stem (or stack)
E = external loop

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