Inhalt

•  
  Motivation and Overview
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   Problem Statement
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   Related Work
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   Summary of Results
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   Structure of the Thesis
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   Future Research
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   Acknowledgments
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  Conventions & Definitions
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   Typographic Conventions
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   Basic Definitions & Notations
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   Programming Languages
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  Concepts & Models in Biology & Biochemistry
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  Introduction
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   RNA Functions
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   RNA Structure Formation
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   RNA Structure Determination
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   RNA Secondary Structure Representation
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   Nearest Neighbor Model & Thermodynamics
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   Molecular Forces
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   Free Energy
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   The Nearest Neighbor Model
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  Structural Representations
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   Data Representations
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   Secondary Structure Validation
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   Graphical Representations
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   Energy Yield
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  Algebraic Dynamic Programming
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  Dynamic Programming
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   The Role of DP in Bioinformatics
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   DP Application Principles
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   An Example: Base Pair Maximization
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   Understanding DP Recurrences
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   Separation of Concerns
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   Search Space
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   Conclusion
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   Algebras
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   Term Algebras
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   Evaluation Algebras
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   Conclusion
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  Grammars & Languages
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   Tree Grammars
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   Yield Grammars
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   DP Search Space
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   Blackboard Notation
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   Conclusion
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   Combinator Parsing
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   Parsers
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   Combinators
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   Filters
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   Memoization
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   Recurrence Derivation
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   Comparison of Recurrences
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  Ambiguity (Zuker's Algorithm)
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   Zukers Description
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   Zukers Algorithm in ADP
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   Ambiguity
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   Types of Ambiguity
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   Avoidance Measures
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   Efficiency
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  Canonicity (Wuchty's Algorithm)
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   Wuchtys Algorithm in ADP
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   Comparison to Zuker's Algorithm
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  Decomposition (Lyngsø's Algorithm)
•  
   Introduction
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   Possible Decompositions
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   Analysis of the Evaluation Function
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   Invariant Formulation
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   Lyngsø's Algorithm in ADP
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   Conclusion
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  Refining the Multiple Loop Energy Model
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   Introduction
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   The Modelling Choice
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   The Dangling-Ends Algorithm in ADP
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   Conclusion
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  Reducing the Conformation Space by Structural Constraints
•  
   Introduction
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   Lonely Pairs
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   The 'No Lonely Pairs' Algorithm in ADP
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   Saturated Structures
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   Discussion
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  Attribute Combinators
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   Bottom-Up Attributes
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   Bottom-Up Attribute Example
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   Top-Down Attribute Example
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   Top-Down Attribute Combinators
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   Saturated Structures in ADP
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   Discussion
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   Local Minima
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  Functions
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   Energy Functions
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  Stacking Region Energies
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   Stacking Energies
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  Hairpin Loop Energies
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   Entropic Term
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   Tetraloop Bonus Energies
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   Mismatch Stacking Energies
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   Entropic Term
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  Bulge Loop Energies
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   Entropic Term
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   Mismatch Stacking Energies
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   Lyngsø's decomposition
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  Multiple Loop Energies
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   Affine Costs
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   Dangling End Energies
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   Combinator Parsing with Attributes
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   Top-Down Attribute Combinators
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   Bottom-Up Attributes
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   2D Graphics Functions
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   Circle Plot
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   Mountain Plot
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   Polygon Plot
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   Examples
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   Utilities
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   Bibliography