sci-biology / vienna-rna

RNA secondary structure prediction and comparison

Official package sites : http://www.tbi.univie.ac.at/~ivo/RNA/ ·

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. 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 and 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 and Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).

v2.1.8 :: 0 :: gentoo

Modified
License
vienna-rna
Keywords
~amd64 ~ppc ~x86
USE flags
doc openmp python static-libs

v2.1.1 :: 0 :: gentoo

Modified
License
vienna-rna
Keywords
amd64 ppc x86
USE flags
doc openmp python static-libs

General

doc
Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
openmp
Build support for the OpenMP (support parallel computing), requires >=sys-devel/gcc-4.2 built with USE="openmp"
python
Add optional support/bindings for the Python language
static-libs
Build static versions of dynamic libraries as well

python_targets

python2_7
Build with Python 2.7

app-portage / elt-patches : Collection of patches for libtool.eclass

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

dev-lang / swig : Simplified Wrapper and Interface Generator

dev-texlive / texlive-latex : TeXLive LaTeX fundamental packages

media-libs / gd : Graphics library for fast image creation

sys-devel / autoconf : Used to create autoconfiguration files

sys-devel / automake : Used to generate Makefile.in from Makefile.am

sys-devel / libtool : A shared library tool for developers

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

dev-texlive / texlive-latex : TeXLive LaTeX fundamental packages

media-libs / gd : Graphics library for fast image creation

529752
sci-biology/vienna-rna-2.1.8[doc] fails to build
591570
sci-biology/vienna-rna-2.1.8 : x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
David Seifert · gentoo
sci-biology/vienna-rna: Remove dev-lang/swig from RDEPEND
Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3856
David Seifert · gentoo
sci-biology/vienna-rna: Fix QA MissingSlotDep
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/vienna-rna: Fix QA MissingSlotDep
Package-Manager: portage-2.2.28
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed