Package: vienna-rna (2.5.1+dfsg-1 and others) [non-free]

[ Source: vienna-rna  ]

RNA sequence analysis

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna.

RNA secondary structure prediction through energy minimization is the most used function in the package. It provides 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, is provided an algorithm to design sequences with a predefined structure (inverse folding). The RNAforester package is a tool for aligning RNA secondary structures and it's user interface integrates to those of the tools of the Vienna RNA package.

Other Packages Related to vienna-rna

• dep: libc6 (>= 2.34) [riscv64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.35) [not riscv64]

• dep: libdlib19.1t64 (>= 19.24+dfsg)

  C++ toolkit for machine learning and computer vision - library

• dep: libgcc-s1 (>= 3.3.1) [not riscv64]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [riscv64]

• dep: libgomp1 (>= 4.9)

  GCC OpenMP (GOMP) support library

• dep: libgsl27 (>= 2.7.1)

  GNU Scientific Library (GSL) -- library package

• dep: libgslcblas0 (>= 2.7.1)

  GNU Scientific Library (GSL) -- blas library package

• dep: liblapack3

  Library of linear algebra routines 3 - shared version

  or liblapack.so.3

  virtual package provided by libatlas3-base, liblapack3, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial

• dep: libmpfr6 (>= 3.1.3)

  multiple precision floating-point computation

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

• rec: readseq

  Conversion between sequence formats

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Architecture	Version	Package Size	Installed Size	Files
amd64	2.5.1+dfsg-1+b1	3,022.9 kB	88,663.0 kB	[list of files]
arm64	2.5.1+dfsg-1+b1	2,717.3 kB	90,786.0 kB	[list of files]
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s390x	2.5.1+dfsg-1+b1	2,862.5 kB	95,374.0 kB	[list of files]