Nussinov78: Nussinov78 using the ADPfusion library.

[ bioinformatics, gpl, library, program ] [ Propose Tags ]

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".

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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 (==0.0.1.2), base (>=4 && <5), BiobaseXNA (==0.6.2.5), mtl (>=2), primitive (>=0.4 && <0.5), PrimitiveArray (==0.2.2.0), vector (>=0.9 && <0.10) [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 2012-07-08T01:37:42Z
Distributions NixOS:0.1.0.0
Executables Nussinov78
Downloads 4313 total (7 in the last 30 days)
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Status Docs uploaded by user
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