The Nussinov78 package

[Tags:gpl, library, program]

The Nussinov78 RNA secondary structure prediction algorithm using the ADPfusion framework.

This algorithm is simple enough to be used as a tutorial-type example. It also shows that efficient code is possible. The ADPfusion code compared to C is slower by a factor of only 1.2. We plan to improve upon this.

A number of helper functions currently present in BioInf.Nussinov78 will later move in their own library.

Build using GHC-7.6.1, the new code generator and llvm for best performance.

For comparison, a version of the algorithm written in C is available under C/nussinov.c. Use at least gcc -O3 nussinov.c.


Dependencies ADPfusion (==0.1.*), base (==4.*), ghc-prim, mtl (>=2), primitive (==0.5.*), PrimitiveArray (==, vector (==0.10.*) [details]
License GPL-3
Copyright Christian Hoener zu Siederdissen, 2011-2012
Author Christian Hoener zu Siederdissen, 2011-2012
Stability experimental
Category Bioinformatics
Home page
Source repository head: git clone git://
Uploaded Wed Nov 7 18:25:18 UTC 2012 by ChristianHoener
Distributions NixOS:
Downloads 1261 total (12 in the last 30 days)
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Status Docs uploaded by user
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