These limitations of the Zuker method and other methods have been largely overcome by using an algorithm originally described by Waterman and Byers (1985) for finding sequence alignments within a certain range of the optimal one by modifications of the trace-back procedure used in dynamic programming.

RNA structure prediction is a method that aims to predict the base-pairing structure of a given RNA sequence. The most common approach for predicting RNA secondary structures is based on thermodynamic models. These models decompose a secondary structure into substructures, called nearest-neighbor loops. Topics include: Types of RNA Structures, RNA Secondary Structure Prediction Methods, Ab Initio Approach, Comparative Approach, Performance Evaluation, Limitations of Prediction, Minimum Free – Energy Method & Stochastic Context – Free Grammars, MFOLD and the Use of Energy... Show more

RNA structure prediction is a method that aims to predict the base-pairing structure of a given RNA sequence. The most common approach for predicting RNA secondary structures is based on thermodynamic models. These models decompose a secondary structure into substructures, called nearest-neighbor loops.

Topics include: Types of RNA Structures, RNA Secondary Structure Prediction Methods, Ab Initio Approach, Comparative Approach, Performance Evaluation, Limitations of Prediction, Minimum Free – Energy Method & Stochastic Context – Free Grammars, MFOLD and the Use of Energy Plot, & Searching Genomes for RNA & RNA Structure Modeling Applications.

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