Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA
targets via post-transcriptional base pair interactions. We determined features that …

Motivation: Currently, the best RNA–RNA interaction prediction tools are based on
approaches that consider both the inter-and intramolecular interactions of hybridizing RNAs …

Abstract Motivation: Predicting RNA–RNA interactions is essential for determining the
function of putative non-coding RNAs. Existing methods for the prediction of interactions are …

The genome of most prokaryotes gives rise to surprisingly complex transcriptomes,
comprising not only protein-coding mRNAs, often organized as operons, but also harbors …

The function of non-coding RNA genes largely depends on their secondary structure and the
interaction with other molecules. Thus, an accurate prediction of secondary structure and …

Motivation: Many computerized methods for RNA–RNA interaction structure prediction have
been developed. Recently, O (N 6) time and O (N 4) space dynamic programming …

IRBIS is a computational pipeline for detecting conserved complementary regions in
unaligned orthologous sequences. Unlike other methods, it follows the “first-fold-then-align” …

Over the last two decades it has become clear that RNA is much more than just a boring
intermediate in protein expression. Ancient RNAs still appear in the core information …

We describe different tools and approaches for RNA–RNA interaction prediction.
Recognition of ncRNA targets is predominantly governed by two principles, namely the …

Prediction of RNA–RNA interaction is a key to elucidating possible functions of small non-
coding RNAs, and a number of computational methods have been proposed to analyze …