What is the main secondary structure of RNA?

The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules.

How do you predict the secondary structure of RNA?

The most popular approach for predicting RNA secondary structures is based on thermodynamic models, such as Turner’s nearest-neighbor model3,4, in which a secondary structure is decomposed into several characteristic substructures, called nearest-neighbor loops, such as hairpin loops, internal loops, bulge loops, base- …

What is an example of secondary structure of RNA?

There are many secondary structure elements of functional importance to biological RNA’s; some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf.

What is the secondary structure of RNA stabilized by?

In the double helical structure of the DNA molecule, two complementary nucleotide strands are held together with hydrogen bonds between the Waston-Crick pairs A-T and C-G.

How does unafold software predict RNA secondary structure?

The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folds and predicts RNA secondary structure and pseudoknots using an entropy model derived from polymer physics.

How is RNAstructure used in siRNA design?

This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction.

How is RNAstructure used for RNA structure prediction?

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities.

How to use ViennaRNA for RNA secondary structure analysis?

…compares RNA family covariance models. A database for the detailed investigation of AU-rich elements. A list of trackhubs ready to be loaded into the UCSC Genome Browser. the Vienna RNA Package, our basic RNA secondary structure analysis software.