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/" /> 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/" /> 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/" /> Product Grammars for Alignment and Folding
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Issue No.03 - May-June (2015 vol.12)
pp: 507-519
Christian Honer zu Siederdissen , Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria
Ivo L. Hofacker , Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria
Peter F. Stadler , Bioinformatics Group of the Department of Computer Science
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 $ {\rm L}^AT_{E}X$ 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/
INDEX TERMS
Grammar, Production, Bioinformatics, Heuristic algorithms, Dynamic programming, Computational biology, IEEE transactions,Haskell, linear grammar, context free grammar, product structure, multiple alignment,Haskell, linear grammar, context free grammar, product structure, multiple alignment
CITATION
Christian Honer zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler, "Product Grammars for Alignment and Folding", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, no. 3, pp. 507-519, May-June 2015, doi:10.1109/TCBB.2014.2326155
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