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This work proposes DUELMERGE, a stable merging algorithm that is asymptotically optimal in the number of comparisons and performs O (n log2 (n) moves. Unlike other partition-based algorithms, we only allow blocks of equal sizes to be swapped, which reduces the number of moves required. We performed experiments comparing DUELMERGE against a number of baselines including RECMERGE, the standard merging solution for programming languages such as C, and some more recent approaches. The results show that our proposed algorithm performs fewer moves than other stable solutions. Experiments employing DUELMERGE within MergeSort confirmed our positive results in terms of moves, comparisons and runtime. [ABSTRACT FROM AUTHOR]

Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics- based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. [ABSTRACT FROM AUTHOR]