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 1.8. We plan to improve upon this.

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

If possible, build using the GHC llvm backend, and GHC-7.2.2. GHC-7.4.x produces very bad code on my system, please benchmark using 7.2.2.

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


Properties

Versions0.0.1.0, 0.0.1.1, 0.0.1.2, 0.0.1.3, 0.1.0.0
DependenciesADPfusion (==0.0.1.1), base (==4.*), BiobaseXNA (==0.6.2.4), mtl (>=2), primitive (==0.4.*), PrimitiveArray (==0.2.1.1), vector (==0.9.*)
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2011-2012
AuthorChristian Hoener zu Siederdissen, 2011-2012
Maintainerchoener@tbi.univie.ac.at
Stabilityexperimental
CategoryBioinformatics
Home pagehttp://www.tbi.univie.ac.at/~choener/adpfusion
Source repositoryhead: git clone git://github.com/choener/Nussinov78
ExecutablesNussinov78
Upload dateSun May 20 13:56:51 UTC 2012
Uploaded byChristianHoener
Downloads393 total (35 in last 30 days)

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