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Many computerized methods for RNA-RNA interaction structure prediction havebeen developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programmingalgorithms have become available that compute the partition function of RNA-RNAinteraction complexes. However, few of these methods incorporate the knowledgeconcerning related sequences, thus relevant evolutionary information is oftenneglected from the structure determination. Therefore, it is of considerablepractical interest to introduce a method taking into consideration boththermodynamic stability and sequence covariation. We present the \emph{apriori} folding algorithm \texttt{ripalign}, whose input consists of two(given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) thepartition function, (2) base-pairing probabilities, (3) hybrid probabilitiesand (4) a set of Boltzmann-sampled suboptimal structures consisting ofcanonical joint structures that are compatible to the alignments. Compared tothe single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign}requires negligible additional memory resource. Furthermore, we incorporatepossible structure constraints as input parameters into our algorithm. Thealgorithm described here is implemented in C as part of the \texttt{rip}package. The supplemental material, source code and input/output files canfreely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}.\section{Contact} Christian Reidys \texttt{duck@santafe.edu}

RNA-RNA interaction prediction based on multiple sequence alignments