Problem 61: RNA Folding
Revision as of 12:06, 1 June 2014 by Krzysztof Onak (talk | contribs)
| Suggested by | Qin Zhang |
|---|---|
| Source | Bertinoro 2014 |
| Short link | https://sublinear.info/61 |
An RNA sequence is a string of letters from the alphabet {A, C, G, U}, where A-U and C-G form pairings. A set of pairings in such a string is said to be non-crossing if there are no pairs of the form $(i, j), (k, l)$ where $i < k < j < l$.
A maximum non-crossing matching is a pairing of A-U and C-G of maximum cardinality that is non-crossing. Given a string, such a matching can be computed in $n^2$ space and $n^3$ time via dynamic programming [Eddy-04].
Note that there is a trivial 2-approximation to the optimal matching. Find the optimal matchings on the A, U and C, G subsequences, and take the larger one. This can be computed in a stream.
Is there a streaming algorithm that yields a factor better than 2 (in a small number of passes)?
