Product grammars for alignment and folding
Editor: Ying Xu Authors: 
Christian Höner Zu Siederdissen, Ivo L. Hofacker, Peter F. StadlerAuthors Info & Claims
Christian Höner Zu Siederdissen, Ivo L. Hofacker, Peter F. StadlerAuthors Info & ClaimsPages 507 - 519
Abstract
We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in LATEX for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf. uni-leipzig.de/Software/gramprod/
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- Product grammars for alignment and folding
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IEEE Computer Society Press
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Publication History
Published: 01 May 2015
Accepted: 10 May 2014
Revised: 29 April 2014
Received: 12 December 2013
Published in TCBB Volume 12, Issue 3
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