| RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding). In case you are using our software for your publications you may want to cite: Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26 |
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/vienna_rna
| Repository package_perl_5_18 revision 35f117d7396b owned by iuc (prior install required) |
| Repository package_gnu_coreutils_8_25 revision a177f177d42f owned by iuc (prior install required) |
| Name | Version | Type | |
|---|---|---|---|
| vienna_rna | 2.1 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Calculate energy of RNA sequences with given secondary structure | 2.1.6.0 | any | |
| calculates locally stable secondary structures of RNA | 2.1.6.0 | any | |
| predicts RNA secondary structures including pseudoknots | 2.1.6.0 | any | |
| Calculate minimum free energy secondary structures and partition function of RNAs | 2.1.6.0 | any | |
| RNA alignment based on sequence base pairing propensities | 2.1.6.0 | any | |
| explore structure space between two reference structures | 2.1.6.0 | any | |
| Calculate RNA sequence from secondary structure | 2.1.6.0 | any | |
| predicts RNA secondary structures including pseudoknots | 2.1.6.0 | any | |
| Calculate minimum free energy secondary structures and partition function on a multiple alignment file | 2.1.6.0 | any | |
| Calculate locally stable secondary structures for a set of aligned RNAs | 2.1.6.0 | any | |
| Calculate secondary structures of two RNAs with dimerization | 2.1.6.0 | any | |
| Draw RNA Secondary Structures | 2.1.6.0 | any | |
| Calculate energies of RNA in a temperature range | 2.1.6.0 | any | |
| Find targets of a query H/ACA snoRNA | 2.1.6.0 | any | |
| Calculate the thermodynamics of RNA-RNA interactions | 2.1.6.0 | any | |
| find binding sites of two RNA alignments | 2.1.6.0 | any | |
| Calculates suboptimal secondary structures of RNAs | 2.1.6.0 | any | |
| Calculate distances between thermodynamic RNA secondary structure ensembles | 2.1.6.0 | any | |
| Calculate distance between secondary structures of two RNAs | 2.1.6.0 | any | |
| Find targets of a query RNA | 2.1.6.0 | any | |
| Compute the structure upon hybridization of two RNA strands | 2.1.6.0 | any | |