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Christian Hoener zu Siederdiss , C. H\ddot{o}ner zu Siederdissen is with the Department of Theoretical Chemistry of the University of Vienna, W\ddot{a}hringerstrasse 17, A-1090 Vienna, Austria (e-mail: choener@tbi.univie.ac.at). SFB F43 MI439/14-1
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 1-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. http://www.bioinf.uni-leipzig.de/Software/gramprod/
INDEX TERMS
Grammar, Production, Bioinformatics, Heuristic algorithms, Dynamic programming, Computational biology, IEEE transactions,Haskell, linear grammar, context free grammar, product structure, multiple alignment
CITATION
Christian Hoener zu Siederdiss, Ivo Hofacker, Peter Stadler, "Product Grammars for Alignment and Folding", IEEE/ACM Transactions on Computational Biology and Bioinformatics, , no. 1, pp. 1, PrePrints PrePrints, doi:10.1109/TCBB.2014.2326155
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