Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository viennarna_rnaalifold
Owner: rnateam
Synopsis: Wrapper for ViennaRNA application RNAalifold.
RNA secondary structure prediction through energy minimization is the most used function in the package. There are three kinds of dynamic programming algorithms for structure prediction provided: 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).
Type: unrestricted
Revision: 7:b63684e40386
This revision can be installed: True
Times cloned / installed: 1645

Contents of this repository

Name Description Version Minimum Galaxy Version
Calculate minimum free energy secondary structures and partition function on a multiple alignment file 2.2.10.1 16.01

Categories
RNA - Utilities for RNA