The GrammarProducts package

[Tags: gpl, library]

An algebra of liner and context-free grammars.

This library provides the implementation of our theory of algebraic operations over linear and context-free grammars. Using algebraic operations, it is possible to construct complex dynamic programming algorithms from simpler atomic grammars.

Our most important contribution is the definition of a product of grammars which naturally leads to alignment-like algorithms on multiple tapes.

An efficient implementation of the resulting grammars is possible via the ADPfusion framework. The FormalGrammars library provides the required Template Haskell machinery. GramarProducts can be integrated as a plugin into the existing transformation from DSL to ADPfusion. Haskell users can just use the QQ function provided in the .QQ module.

Alternatively, the resulting grammars can also be pretty-printed in various ways (LaTeX, ANSI, Haskell module with signature and grammar).

Formal background can be found in two papers:

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
Product Grammars for Alignment and Folding.
2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99.
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790

and

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
How to Multiply Dynamic Programming Algorithms
Brazilian Symposium on Bioinformatics (BSB 2013)
Lecture Notes in Bioinformatics 8213, Springer, Heidelberg

Properties

Versions0.0.0.2, 0.0.0.3, 0.0.0.4, 0.1.0.0
Change logchangelog.md
DependenciesADPfusion (==0.4.0.*), ansi-wl-pprint (==0.6.*), base (>=4.7 && <4.9), bytestring (==0.10.*), containers (==0.5.*), data-default (==0.5.*), FormalGrammars (==0.2.0.*), GrammarProducts, lens (==4.*), newtype (==0.2.*), parsers (==0.12.*), PrimitiveArray (==0.6.0.*), semigroups (>=0.15 && <0.17), template-haskell (==2.*), transformers (==0.4.*), trifecta (==1.5.*), vector (==0.10.*)
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2013-2015
AuthorChristian Hoener zu Siederdissen, 2013-2015
Maintainerchoener@bioinf.uni-leipzig.de
Stabilityexperimental
CategoryFormal Languages, Bioinformatics
Home pagehttp://www.bioinf.uni-leipzig.de/gADP/
Source repositoryhead: git clone git://github.com/choener/GrammarProducts
ExecutablesAlignGlobal
UploadedThu May 7 17:01:55 UTC 2015 by ChristianHoener
DistributionsNixOS:0.1.0.0
Downloads549 total (51 in last 30 days)
StatusDocs available [build log]
Last success reported on 2015-05-07 [all 1 reports]

Modules

[Index]

Flags

NameDescriptionDefault
examplesbuild the examples (only Needleman-Wunsch for now)Disabled
llvmbuild using LLVMDisabled

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

Downloads

Maintainers' corner

For package maintainers and hackage trustees