Vienna RNA Package 1.8.3

News in short

• Current version of the Vienna RNA Package is 1.8.3, download the source distribution here.
  Some recently added features:
• The RNAup program for computing RNA-RNA interactions is now included.
• Folding of circular RNAs is now supported in many of the programs
• support for computing hybrid structures using RNAcofold, RNAup, RNAduplex, and RNAaliduplex.
• stochastic backtracking to produce Boltzmann weighted ensembles of suboptimal structures (try RNAsubopt -p 10).
• Local versions of the folding algorithms for scanning large sequences (genomes): RNALfold and RNAplfold
  RNAplfold can now be used to compute local accessibilities
• Several new utilities e.g. for color annotated structure plots, consensus structures and alignments.
• The Vienna RNA package now distributes two related but separate pieces of software:
  • The RNAforester, written by Matthias Hoechsmann , computes tree-alignments of RNA structures
  • The kinfold program explores the folding kinetics of RNA molecules through simulation of stochastic folding trajectories.
• Windows users see our page about running the Vienna RNA package under Windows, including a several precompiled binaries.

General information

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 & 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).

Documentation

For a detailed information, take a look at the HTML versions of the man pages for the programs and the manual of the library below.

• RNAfold -- predict minimum energy secondary structures and pair probabilities
• RNAeval -- evaluate energy of RNA secondary structures
• RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
• RNAinverse -- inverse fold (design) sequences with predefined structure
• RNAdistance -- compare secondary structures
• RNApdist -- compare base pair probabilities
• RNAsubopt -- complete suboptimal folding
• RNAplot -- RNA structure drawings in PostScript, SVG, or GML
• RNAcofold -- predict hybrid structure of two sequences
• RNAduplex -- predict possible hybridization sites between two sequences
• RNAalifold -- predict the consensus structure of several aligned sequences
• RNALfold -- predict locally stable structure of long sequences
• RNAplfold -- compute average pair probabilities for local base pairs in long sequences
• RNApaln -- fast structural alignment of RNA sequences using string alignments
• Several small but helpful Perl Utilities

If you want to include our code into your own programs, you should read the documentation for the RNAlib library.
When installing from source, see the installation instructions.

The package is free software and can be downloaded as C source code that should be easy to compile on almost any flavor of Unix and Linux. See the README file for details.

维也纳大学RNA二级结构预测与比较软件包，全部下载共计5.8M。
包括以下软件：
RNAfold预测最小能量二级结构，并给出图像；
RNAeval估算RNA二级结构的能量值；
RNAheat计算一个RNA序列的融解曲线；
RNAinverse预定结构的序列的反转折叠；
RNAdistance比较二级结构；
RNApdist比较碱基对的概率；
RNAsubopt完善次优折叠。
还有RNAalifold和RNAplot。

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