I have a question about the
mountain.pl script：How to extract the pair probabilities from
*_dp.ps file using mountain.pl?
According to the descritpion of
mountain.pl script: definition of pair probabilities for base i is the mean pair probabilities enclode the base i. But the
mountain.pl count the sum instead. This is the reason why
mountain.pl failed to process
$ RNAplfold --version RNAplfold 2.4.14 $ cat 5S.seq > 5S rRNA from methanospirillum hungatii UCAAUAGCGGCCACAGCAGGUGUGUCACACCCGUUCCCAUUCCGAACACGGAAGUUAAGACACCUCACGUGGAUGACGGUACUGAGGUACGCGAGUCCUCGGGAAAUCAUCCUCGCUGCUAUUGUU $ RNAplfold -W 70 -u 28 < 5S.seq # output files: 5S_dp.ps, 5S_lunp $ ./ViennaRNA-2.4.14/src/Utils/mountain.pl 5S_dp.ps Can't take log of -0.036633 at ./ViennaRNA-2.4.14/src/Utils/mountain.pl line 66, <> line 385.
Here are the line report error in
# line-66 of mountain.pl $sp[$i] += (1-$pp[$i])*log(abs(1-$pp[$i]));
The description of
# produce Pauline Hogeweg's mountain representation *_dp.ps files # writes 3 sets of x y data separated by a "&" # the first two sets are mountain representations from base pair probabilities # and mfe structure, respectively. # definition: mm[i],mp[i] = (mean) number of base pairs enclosing base i # third set a measure of well-definedness: the entropy of the pair probs of # base i, sp[i] = -Sum p_i * ln(p_i). Well-defined regions have low entropy.