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 1.2. 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".




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Versions [RSS],,,,
Dependencies ADPfusion (>=0.1 && <0.2), base (>=4 && <5), ghc-prim, mtl (>=2), primitive (>=0.5 && <0.6), PrimitiveArray (==, 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
Category Bioinformatics
Home page
Source repo head: git clone git://
Uploaded by ChristianHoener at 2012-11-07T18:25:18Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables Nussinov78
Downloads 4558 total (11 in the last 30 days)
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Status Docs uploaded by user
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