Nussinov78: Nussinov78 using the ADPfusion library.

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".

Modules

[Index]

Flags

Automatic Flags

Name	Description	Default
llvm	build using llvm backend	Enabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

Downloads

• Nussinov78-0.0.1.2.tar.gz [browse] (Cabal source package)
• Package description (as included in the package)

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Package maintainers

• ChristianHoener

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