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Modeling Biological Structures Via Abstract Grammars To Solve Common Problems In Computational Biology, David J. Russell
Modeling Biological Structures Via Abstract Grammars To Solve Common Problems In Computational Biology, David J. Russell
Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research
Grammars are generally understood to be the set of rules that define the relationships between elements of a language. However, grammars can also be used to elucidate structural relationships within sequences constructed from any finite alphabet. In this work abstract grammars are used to model the primary and secondary structures present in biological data. These grammar models are inferred and applied to efficiently solve various sequence analysis problems in computational biology, including multiple sequence alignment, fragment assembly, database redundancy removal, and structural prediction.
The primary structures, or sequential ordering of symbols, of biological data are first modeled with Lempel-Ziv (LZ) …