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The latest version of GrammarProducts is 0.2.0.0-0.

GrammarProducts

Version 0.1.0.0 revision 0 uploaded by ChristianHoener.

Package meta

Synopsis
Grammar products and higher-dimensional grammars
Description

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
Author
Christian Hoener zu Siederdissen, 2013-2015
Bug reports
n/a
Category
Formal Languages, Bioinformatics
Copyright
Christian Hoener zu Siederdissen, 2013-2015
Homepage
http://www.bioinf.uni-leipzig.de/gADP/
Maintainer
choener@bioinf.uni-leipzig.de
Package URL
n/a
Stability
experimental

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