Package: vienna-rna (2.6.4+dfsg-1) [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 (>= 2.38)

  Libreria C GNU: librerie condivise
  also a virtual package provided by libc6-udeb

• dep: libdlib19.2 (>= 19.24.4+dfsg)

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

• dep: libgcc-s1 (>= 3.4)

  libreria di supporto a GCC

• dep: libgomp1 (>= 4.9)

  libreria di supporto GOMP (GCC OpenMP)

• dep: libgsl28 (>= 2.8+dfsg)

  GNU Scientific Library (GSL) -- pacchetto della libreria

• dep: libgslcblas0 (>= 2.8)

  libreria scientifica GNU (GSL) -- pacchetto di libreria blas

• dep: liblapack3

  libreria di routine per l'algebra lineare 3 - versione condivisa

  or liblapack.so.3

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

• dep: libmpfr6 (>= 3.1.3)

  calcoli in virgola mobile a precisione multipla

• dep: libstdc++6 (>= 13.1)

  libreria GNU Standard C++, versione 3

• rec: readseq

  conversione tra formati di sequenze

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