Interpretation of RNAplfold

Question

[Aishwarya Kulkarni]

Hi I ran RNAplfold as RNAplfold -W 60 -u 11 < trial.fa on a sequence of length 71, it gives me an output of matrix(in the file with extension '_lunp'), with 71 rows and 11 columns, however I didn't quiet get the concept.According to the documentation it says that it will calculate the average probability over each u of 11 length over sliding window of length 60, if that's the case then why is it that in the matrix the first 10 rows have NA in their 11 length windows:

#i$ l=1 2   3   4   5   6   7   8   9   10  11
  1 0.9469881   NA  NA  NA  NA  NA  NA  NA  NA  NA  NA
  2 0.7428546   0.7108948   NA  NA  NA  NA  NA  NA  NA  NA  NA
  3 0.7833689   0.6985533   0.6691537   NA  NA  NA  NA  NA  NA  NA  NA
  4 0.8540909   0.7242232   0.655665    0.6532912   NA  NA  NA  NA  NA  NA  NA
  5 0.8320361   0.7807689   0.686046    0.6210906   0.6206707   NA  NA  NA  NA  NA  NA
  6 0.9145157   0.7697201   0.7289685   0.6372758   0.5771261   0.5777204   NA  NA  NA  NA  NA
  7 0.9481671   0.9134377   0.7694369   0.7286978   0.6370939   0.5769615   0.5775573   NA  NA  NA  NA
  8 0.9930493   0.9427189   0.9119256   0.7681018   0.7271193   0.6369164   0.5768006   0.577397    NA  NA  NA
  9 0.996136    0.9919387   0.9416257   0.9109458   0.7673214   0.7262351   0.6367918   0.5766883   0.5772853   NA  NA
 10 0.5856886   0.5843086   0.5835655   0.5382947   0.5172792   0.4713382   0.4463127   0.4205373   0.3834285   0.3872539   NA

and also why would the last row contain average probabilities over 11 nucleotides when 71st sequence is the last one?

71  0.0572429   0.006454323 0.005939727 0.005937336 0.005934025 0.005908198 0.005830827 0.005815964 0.005814055 0.005804212 0.005767331

Thanks

Answer 1

[Asaf]

From the man page:

The output is a plain text matrix containing on each line a position i followed by the probability that i is unpaired, [i-1..i] is unpaired [i-2..i] is unpaired and so on to the probability that [i-x+1..i] is unpaired.

So the 11th row contains the probability that i-11:I is unpaired, first 10 rows are invalid.

[Aishwarya Kulkarni]

So does that mean that for the probability of the first 11 mer being unpaired would be under 11 th row and 11 the column i.e at 11-11+1...11? for instance

11 0.6214644 0.5804635 0.5794147 0.5787987 0.5336643 0.512956 0.4683483 0.4437102 0.4185386 0.381642 0.3854975

The last one will be the probability of first 11 mer being unpaired correct?

[Asaf]

Yes, it seems so.....