The Nussinov78 package
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.*) |
| 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 | git clone git://github.com/choener/Nussinov78 |
| Executables | Nussinov78 |
| Upload date | Wed Nov 7 18:25:18 UTC 2012 |
| Uploaded by | ChristianHoener |
| Built on | ghc-7.6 |
Modules
- BioInf
Downloads
- Nussinov78-0.1.0.0.tar.gz (Cabal source package)
- package description (included in the package)