GrammarProducts: Grammar products and higher-dimensional grammars

[ bioinformatics, formal-languages, gpl, library ] [ Propose Tags ]

generalized Algebraic Dynamic Programming

An algebra of linear 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 (ANSI, Haskell module with signature and grammar).

The formal background can be found in two papers given in the README. The gADP homepage has further details, tutorials, examples.

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Dependencies ADPfusion (>=0.6.0 && <0.6.1), ansi-wl-pprint (>=0.6), base (>=4.7 && <5.0), bytestring (>=0.10), containers (>=0.5), data-default (>=0.5), FormalGrammars (>=0.4.0 && <0.4.1), lens (>=4), newtype (>=0.2), parsers (>=0.12), PrimitiveArray (>=0.10.0 && <0.10.1), semigroups (>=0.15), template-haskell (>=2), transformers (>=0.4), trifecta (>= && <2.1) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2013-2019
Author Christian Hoener zu Siederdissen, 2013-2019
Category Formal Languages, Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2019-10-02T09:59:32Z
Reverse Dependencies 4 direct, 1 indirect [details]
Executables AlignGlobal
Downloads 7385 total (20 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2019-10-02 [all 1 reports]

Readme for GrammarProducts-

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GrammarProducts: Products of formal languages

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generalized Algebraic Dynamic Programming Homepage

An abstract algebra for linear and context-free grammars.

  1. 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
  2. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
    How to Multiply Dynamic Programming Algorithms
    2013, Brazilian Symposium on Bioinformatics (BSB 2013)
    Lecture Notes in Bioinformatics 8213. Springer, Heidelberg.
    paper preprint


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany