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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build using llvm backend


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Dependencies ADPfusion (==, base (>=4 && <5), BiobaseXNA (==, mtl (>=2), primitive (>=0.4 && <0.5), PrimitiveArray (==, 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
Category Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2012-07-08T01:37:42Z
Distributions NixOS:
Executables Nussinov78
Downloads 4313 total (7 in the last 30 days)
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Status Docs uploaded by user
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