Nussinov78: Nussinov78 using the ADPfusion library.
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".
Downloads
- Nussinov78-0.1.0.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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| Versions [RSS] | 0.0.1.0, 0.0.1.1, 0.0.1.2, 0.0.1.3, 0.1.0.0 |
|---|---|
| Dependencies | ADPfusion (>=0.1 && <0.2), base (>=4 && <5), ghc-prim, mtl (>=2), primitive (>=0.5 && <0.6), PrimitiveArray (==0.4.0.0), vector (>=0.10 && <0.11) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2011-2012 |
| Author | Christian Hoener zu Siederdissen, 2011-2012 |
| Maintainer | choener@tbi.univie.ac.at |
| Category | Bioinformatics |
| Home page | http://www.tbi.univie.ac.at/~choener/adpfusion |
| Source repo | head: git clone git://github.com/choener/Nussinov78 |
| Uploaded | by ChristianHoener at 2012-11-07T18:25:18Z |
| Distributions | |
| Reverse Dependencies | 1 direct, 0 indirect [details] |
| Executables | Nussinov78 |
| Downloads | 4618 total (13 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs uploaded by user Build status unknown [no reports yet] |