Question: How to extract the pair probabilities from *_dp.ps file using mountain.pl?

0

wm •

**490**wrote: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`

output `*_dp.ps`

.

```
$ 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 `mountain.pl`

:

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

The description of `mountain.pl`

script:

```
# 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.
```