RNA structure is crucial for gene regulation and function. In the past, transcriptomes have
largely been parsed by primary sequences and expression levels, but it is now becoming …

The information that can be obtained from the secondary structure of the nuclear ribosomal
internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this …

Background Secondary structure forms an important intermediate level of description of
nucleic acids that encapsulates the dominating part of the folding energy, is often well …

In this paper we survey methods for performing a comparative graph analysis and explain
the history, foundations and differences of such techniques of the last 50 years. While …

Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic
regions containing potential structural ncRNAs. The analysis of these data requires highly …

Many of the known microRNAs are encoded in polycistronic transcripts. Here, we reconstruct
the evolutionary history of the mir17 microRNA clusters which consist of miR-17, miR-18 …

Background The prediction of a consensus structure for a set of related RNAs is an important
first step for subsequent analyses. RNAalifold, which computes the minimum energy …

The RFAM database defines families of ncRNAs by means of sequence similarities that are
sufficient to establish homology. In some cases, such as microRNAs and box H/ACA …

The ongoing characterization of novel species creates the need for a molecular marker
which can be used for species-and, simultaneously, for mega-systematics. Recently, the use …

Motivation: The recent discoveries of large numbers of non-coding RNAs and computational
advances in genome-scale RNA search create a need for tools for automatic, high quality …