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

Versions 0.0.1.0, 0.0.1.1, 0.0.1.2, 0.0.1.3, 0.1.0.0
Dependencies ADPfusion (==0.0.1.2), base (==4.*), BiobaseXNA (==0.6.2.5), mtl (>=2), primitive (==0.4.*), PrimitiveArray (==0.2.2.0), vector (==0.9.*) [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 Sun Jul 8 01:37:42 UTC 2012 by ChristianHoener
Distributions NixOS:0.1.0.0
Downloads 1249 total (7 in the last 30 days)
Votes
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Status Docs uploaded by user
Build status unknown [no reports yet]

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NameDescriptionDefaultType
llvmbuild using llvm backendEnabledAutomatic

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