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The ladder distance (LD) between residue $i$ and residue $j$ is the minimum number of base pairs (created due to secondary structure of the ssRNA) one has to cross when going from $i$ to $j$.

The Maximum Ladder Distance of an ssRNA molecule is the maximum ladder distance between any two of the residues of this molecule[*].

Given the secondary structure of an ssRNA molecule in dot-bracket notation (e.g. by RNAfold), how can I calculate the Maximum Ladder Distance of this molecule?

Below is an illustration from [*]. The MLD is 11, since this is the number of basepairs on the yellow line.

The dot-bracket notation for this molecule would be

..(((((.......))...((.((((((.......))))))..)).)).

Example MLD for a ssRNA molecule

*: Yoffe AM, Prinsen P, Gopal A, Knobler CM, Gelbart WM, et al. (2008) Predicting the sizes of large RNA molecules. Proc Natl Acad Sci U S A 105: 16153–16158

This question was originally posted in the biology stackexchange: How to calculate the Maximum Ladder Distance (MLD) of ssRNA from Dot-Bracket notation?

terdon
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user17291
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  • Since your question from [biology.se] has been migrated here, along with its answer, I closed this as a duplicate of the migrated one. However, it looks like you have created a separate account for this site, so your question doesn't appear as though it belong to you. Please see https://bioinformatics.stackexchange.com/help/merging-accounts – terdon Apr 05 '23 at 14:13

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