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".

Dependencies ADPfusion (==, base (==4.*), BiobaseXNA (==, mtl, primitive (==0.4.*), PrimitiveArray (==, vector (==0.9.*) [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 Sun Mar 25 01:36:37 UTC 2012
Distributions NixOS:
Executables Nussinov78
Downloads 2175 total (19 in the last 30 days)
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build using llvm backend


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