Ribonucleic acid (RNA) is a nucleic acid polymer that plays several important roles in the cell.
As for proteins, the three dimensional shape of an RNA molecule is important for its molecular function. A number of tertiary RNA structures are know from crystallography but de novo prediction of tertiary structures is not possible with current methods. However, as for proteins RNA tertiary structures can be characterized by secondary structural elements which are hydrogen bonds within the molecule that form several recognizable "domains" of secondary structure like stems, hairpin loops, bulges and internal loops. A large part of the functional information is thus contained in the secondary structure of the RNA molecule, as shown by the high degree of base-pair conservation observed in the evolution of RNA molecules.
Computational prediction of RNA secondary structure is a well defined problem and a large body of work has been done to refine prediction algorithms and to experimentally estimate the relevant biological parameters.
In CLC Genomics Workbench we offer the user a number of tools for analyzing and displaying RNA structures. These include:
- Secondary structure prediction using state-of-the-art algorithms and parameters
- Calculation of full partition function to assign probabilities to structural elements and hypotheses
- Scanning of large sequences to find local structure signal
- Inclusion of experimental constraints to the folding process
- Advanced viewing and editing of secondary structures and structure information
- RNA secondary structure prediction
- View and edit secondary structures
- Evaluate structure hypothesis
- Structure Scanning Plot
- Bioinformatics explained: RNA structure prediction by minimum free energy minimization