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choener / FormalGrammars

Context-free and linear grammars in Haskell (parsing, pretty-printing, embedded DSL)
http://www.bioinf.uni-leipzig.de/Software/gADP/
GNU General Public License v3.0
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Please provide examples in repository #3

Open krcurtis opened 4 years ago

krcurtis commented 4 years ago

Hi,

Would you kindly add the tutorial and examples to this repository? I've tried going to:

but this appears empty.

I would like to apply the package to parse grammars written in EBNF. Also it sounds like it might be possible to apply the package to look at RNA secondary structure. I would like to try looking at 16S RNA for bacteria which has several strongly conserved regions across bacteria, where the variable regions are used for organism identification.

Thanks!

choener commented 4 years ago

The original goal with ADPfusion was to simplify writing algorithms for RNA secondary structure prediction. I am currently separating out functionality. ADPfusionSubword will contain the tools to write the type of algorithm you want to design, but will require a couple of weeks before it is on hackage, since I am currently mostly away from work.

A number of supporting libraries on hackage of the type Biobase* have functionality to deal with biosequences, secondary structure, and other things.

Furthermore, there are bindings to the ViennaRNA package, and a Turner energy model.

I'll close this once I have uploaded the new libraries and updated the tutorial.