SCFGs in RNA secondary structure prediction: A hands-on approach

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

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.

Original languageEnglish
JournalMethods in Molecular Biology
Volume1097
Pages (from-to)143-162
Number of pages20
ISSN1064-3745
DOIs
Publication statusPublished - 1 Jan 2014

    Research areas

  • CYK algorithm, Inside–outside algorithm, Pfold, SCFGs

See relations at Aarhus University Citationformats

ID: 129292494