MOTIVATION RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system fully automatically generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space. RESULTS R...

Summary: We present a web server dedicated to the comparison of RNA secondary structures. This server allows to compare pairs of RNA secondary structures and to search, for a given RNA secondary structure, RNA genes with similar structures in a large database of RNA structures. The comparison and search are performed using an edit distance algorithm that considers a wide range of edit operation...

background: genomic dna was isolated from parabronema skrjabini . rrna region was amplified and sequenced. methods : the rna secondary structure was predicted using mfold software (http://mfold.rit.albany.edu). the secondary structure with bulge, hairpins, helices, interior, external and multi loops was predicted for 5.8srdna of our sequence of p. skrjabini and a sequence of p. skrjabini and tw...

Structured RNAs play an essential role in chromosome maintenance, RNA processing, protein biosynthesis, and protein transport. To understand RNA function in these diverse biological systems, the rules for RNA folding and recognition must be learned. Recent crystal structures of hammerhead ribozymes, a group I intron domain, and RNA duplexes provide new insights into the principles of RNA foldin...

In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by Jo...

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure we want to find a sequence that has a certain structure as its ground state. If such a sequence exists, the structure is called designable. We have implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact...

The view of RNA as simple information transfer molecule has been continuously challenged since the discovery of ribozymes, a class of RNA molecules with enzyme-like function. Moreover, the recent discovery of tiny RNA molecules such as RNAs and small interfering RNA, is transforming our thinking about how gene expression is regulated. Thus, RNA molecules are now known to carry a large repertory...

Background: RNA molecules play many important regulatory, catalytic and structural <span style="font-variant: normal; font-style: norma...

Understanding secondary structures of RNAs helps to determine their chemical and biological properties. Only a small number of RNA structures have been determined currently since such structure determination experiments are timeconsuming and expensive. As a result, scientists start to rely on RNA secondary structure prediction. Unlike protein structure prediction, predicting RNA secondary struc...