Question: How to extract the pair probabilities from * file using
gravatar for wm
10 months ago by
wm490 wrote:

I have a question about the script:How to extract the pair probabilities from * file using

According to the descritpion of script: definition of pair probabilities for base i is the mean pair probabilities enclode the base i. But the count the sum instead. This is the reason why failed to process RNAplfold output *

$ RNAplfold --version 
RNAplfold 2.4.14

$ cat 5S.seq
> 5S rRNA from methanospirillum hungatii

$ RNAplfold -W 70 -u 28 < 5S.seq # output files:, 5S_lunp
$ ./ViennaRNA-2.4.14/src/Utils/
Can't take log of -0.036633 at ./ViennaRNA-2.4.14/src/Utils/ line 66, <> line 385.

Here are the line report error in

# line-66 of
$sp[$i] += (1-$pp[$i])*log(abs(1-$pp[$i]));

The description of script:

# produce Pauline Hogeweg's mountain representation * 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.
secondary structure rna • 173 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by wm490
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