An Optimized Parsing Algorithm Well Suited to RNA Folding

An optimized parsing algorithm well suited to RNA

The application of stochastic context-free grammars to the determination of RNA foldings allows a simple description of the sub-class of sought secondary structures, but it needs eecient parsing algorithms. The more classic thermodynamic model of folding, popularized by Zuker under the framework of dynamic programming algorithms, allows an easy computation of foldings but its use is delicate wh...

Relation Between RNA Sequences, Structures, and Shapes via Variation Networks

Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...

An improved joint model: POS tagging and dependency parsing

Dependency parsing is a way of syntactic parsing and a natural language that automatically analyzes the dependency structure of sentences, and the input for each sentence creates a dependency graph. Part-Of-Speech (POS) tagging is a prerequisite for dependency parsing. Generally, dependency parsers do the POS tagging task along with dependency parsing in a pipeline mode. Unfortunately, in pipel...

An E cient Parser Well Suited to RNA Folding

Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding

Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA ...