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RNAFold: RNA secondary structure prediction
RNAfold v2 using the ADPfusion library. The RNAfold algorithm is used to determine how fast we can be compared to a highly optimized C program.
Please use GHC 7.6 or newer.
NOTE I'd like to rename this package to RNAfold, like the C implementation. Do not install "globally", especially if you normally use RNAfold from the ViennaRNA package, for obvious reasons.
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| Versions [RSS] | 0.0.2.1, 1.99.1.0, 1.99.1.1, 1.99.1.2, 1.99.1.3, 1.99.3.4 |
|---|---|
| Dependencies | ADPfusion (>=0.2.0.0), base (>=4 && <5), BiobaseTurner (>=0.3.1.1), BiobaseVienna (>=0.3), BiobaseXNA (>=0.7), cmdargs (>=0.10), containers, deepseq (>=1.3), lens (>=3.8), primitive (>=0.5), PrimitiveArray (>=0.5), repa (>=3.2), RNAFold, strict (>=0.3.2), vector (>=0.10) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2010-2013 |
| Author | Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al (ViennaRNA), 2010-2013 |
| Maintainer | choener@tbi.univie.ac.at |
| Uploaded | by ChristianHoener at 2013-12-06T23:47:37Z |
| Category | Bioinformatics |
| Home page | https://www.tbi.univie.ac.at/~choener/adpfusion |
| Source repo | head: git clone git://github.com/choener/RNAfold |
| Distributions | |
| Reverse Dependencies | 2 direct, 0 indirect [details] |
| Executables | RNAEval, RNAFold |
| Downloads | 6423 total (20 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Successful builds reported [all 1 reports] |
Readme for RNAFold-1.99.3.4
[back to package description]ViennaRNA RNAfold v2, MFE variant using the ADPfusion library
Introduction
This algorithm is the second, and much larger, test case for ADPfusion. We implement "RNAfold v2" in the MFE variant using "-d2" dangles. Both a library version and an executable are created. The "RNAFold" binary expects single sequences, one per line. Backtracking tracks all co-optimal structures.
Installation
A simple "cabal update && cabal-dev install RNAFold" should be enough.
Runtime notes
Using Haskell and ADPfusion, we come to within x3-x4 for this package. Between the initial test case / submission (in 0.0.0.3) I have traded in some performance improvements for much better readability in BioInf.RNAfold.Energy. The C version of RNAfold employs some other methods to improve performance. Consider:
base -~+ inner-1 +~- base base -~+ inner-2 +~- base
where it is advantageous to calculate the outer basepair only once, not twice as we are doing. It is probably better to try to improve the handling of fusioned code and/or final assembler generation than finding calculations common to different parts of CFG's.