{"added":null,"apiVersion":1,"behindSince":null,"buildDepends":[],"categories":["biology"],"comment":"Alignment tools for the structural analysis of RNA","compare":null,"dependentCount":null,"description":"The ViennaRNA Package consists of a C code library and several stand-alone\nprograms for the prediction and comparison of RNA secondary structures.\n\nRNA secondary structure prediction through energy minimization is the most used\nfunction in the package. We provide three kinds of dynamic programming\nalgorithms for structure prediction: the minimum free energy algorithm of\n(Zuker \u0026 Stiegler 1981) which yields a single optimal structure, the partition\nfunction algorithm of (McCaskill 1990) which calculates base pair probabilities\nin the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty\net.al 1999) which generates all suboptimal structures within a given energy\nrange of the optimal energy. For secondary structure comparison, the package\ncontains several measures of distance (dissimilarities) using either string\nalignment or tree-editing (Shapiro \u0026 Zhang 1990). Finally, we provide an\nalgorithm to design sequences with a predefined structure (inverse folding).","flavors":[],"html":"https://daemonports.org/dragonfly/biology/viennarna/","kind":"port","lastUpdate":null,"license":["ViennaRNALicense"],"maintainer":"yuri@FreeBSD.org","name":"viennarna","newest":false,"newestVersion":"2.7.2","noVulnData":false,"origin":"biology/viennarna","otherSystems":[{"maintainer":"yuri@FreeBSD.org","newest":true,"origin":"biology/viennarna","path":"/biology/viennarna/","system":"FreeBSD","version":"2.7.2"},{"maintainer":"yuri@FreeBSD.org","newest":true,"noVulnData":true,"origin":"biology/viennarna","path":"","system":"HardenedBSD","version":"2.7.2"},{"maintainer":"yuri@FreeBSD.org","newest":true,"noVulnData":true,"origin":"biology/viennarna","path":"","system":"GhostBSD","version":"2.7.2"}],"packages":null,"pkgName":"viennarna-2.7.0_1","related":null,"repository":"DPorts","requiredBy":[],"requiredByCount":0,"runDepends":["lang/gcc11","lang/perl5.36","math/gmp","math/gsl","math/lapack","math/mpfr","print/indexinfo","x11/libICE","x11/libX11","x11/libXext"],"status":null,"system":"dragonfly","systemLabel":"DragonFly","version":"2.7.0_1","versions":null,"vulnerabilities":null,"www":"https://www.tbi.univie.ac.at/RNA/"}