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.

Properties

Versions 0.0.1.0, 0.0.1.1, 0.0.1.2, 0.0.1.3, 0.1.0.0
Dependencies ADPfusion (==0.1.*), base (==4.*), ghc-prim, mtl (>=2), primitive (==0.5.*), PrimitiveArray (==0.4.0.0), vector (==0.10.*) [details]
License GPL-3
Copyright Christian Hoener zu Siederdissen, 2011-2012
Author Christian Hoener zu Siederdissen, 2011-2012
Maintainer choener@tbi.univie.ac.at
Stability experimental
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/adpfusion
Source repository head: git clone git://github.com/choener/Nussinov78
Uploaded Wed Nov 7 18:25:18 UTC 2012 by ChristianHoener
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Downloads 1204 total (11 in the last 30 days)
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