SCFGs in RNA Secondary Structure Prediction: A Hands-on Approach
| Autor: | Zsuzsanna Sükösd, Ebbe Sloth Andersen, Rune B. Lyngsø |
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| Rok vydání: | 2013 |
| Předmět: |
Grammar
business.industry Computer science media_common.quotation_subject Context (language use) computer.software_genre TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES Rule-based machine translation Quality (business) Synchronous context-free grammar Artificial intelligence business computer Rna secondary structure prediction Natural language Natural language processing media_common |
| Zdroj: | Methods in Molecular Biology ISBN: 9781627037082 |
| Popis: | Stochastic context-free grammars (SCFGs) were first established in the context of natural language modelling, and only later found their applications in RNA secondary structure prediction. In this chapter, we discuss the basic SCFG algorithms (CYK and inside-outside algorithms) in an application-centered manner and use the pfold grammar as a case study to show how the algorithms can be adapted to a grammar in a nonstandard form. We extend our discussion to the use of grammars with additional information (such as evolutionary information) to improve the quality of predictions. Finally, we provide a brief survey of programs that use stochastic context-free grammars for RNA secondary structure prediction and modelling. |
| Databáze: | OpenAIRE |
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