# Teaching - hybrid-only : max. intermol. bps

The identification of an optimal RNA-RNA interaction

Here, in order to prepare the computation of accessibility-based interaction prediction, the following

*without*consideration of intramolecular base pairs can be done efficiently in $O(nm)$ time and space for two RNA sequences $S^{1}$ and $S^{2}$ of lengths $n$ and $m$, resp., (Brian Tjaden et al., 2006). For a Nussinov-like interaction prediction, a dynamic programming table $H$ is filled via the*prefix-based*recursion$H_{i,j}=\max\begin{cases} H_{i-1,j-1}+1 & \text{if }S^{1}_{i},S^{2}_{j}\text{ compl. base pair}\\ H_{i-1,j} \\ H_{i,j-1} \\ 0 \end{cases}$,

where an entry $H_{i,j}$ provides the maximal number of intermolecular
base pairs for the prefixes $S^{1}_{1..i}$ and $S^{2}_{1..j}$.
Note, this recursion is a variant of a local
Smith-Waterman (1981)
sequence alignment with special scoring, where only
Watson-Crick as well as GU base pairs are considered complementary and thus similiar.
A traceback from the entry $H_{i,j}$ with the highest value provides
an according optimal interaction.
Here, in order to prepare the computation of accessibility-based interaction prediction, the following

*interval-based*recursion is used to identify the RNA-RNA interaction with the maximal number of intermolecular base pairs. To this end, the four-dimensional table $D$ is filled, where an entry $D^{i,k}_{j,l}$ represents the maximal number of base pairs for the sequence intervals $S^{1}_{i..k}$ and $S^{2}_{j..l}$ under the condition that both interval ends are forming the intermolecular base pairs $(S^{1}_{i},S^{2}_{j})$ and $(S^{1}_{k},S^{2}_{l})$. A list of up to 15 maximal base pair RNA-RNA interactions is provided via exhaustive traceback for all table entries with maximal value, i.e. $D^{i,k}_{j,l}=\max(D)$.RNA sequence $S^{1}$:

RNA sequence $S^{2}$:

## Visualization of interacting base pairs (selected structure)

Due to the four-dimensionality of $D$, we only list the optimal
hybrid structures (up to 15). On selection, the intermolecular base pairs are
visualized.

Possible Structures |
---|

The box provides an ASCII representation of the interacting
base pairs of the selected structure with $S^{1}$ on top and $S^{2}$
on the bottom.
Note, sequence $S^{2}$ is reversed (running from right ($5'$) to left
($3'$)) within this representation.
Note further, if no interacting
base pairs are present, no visualization is done.