Editing Probabilistic context-free grammar (section)

====Implementations====
RNA secondary structure implementations based on PCFG approaches can be utilized in :
* Finding consensus structure by optimizing structure joint probabilities over MSA.<ref name="Knudsen 2003" /><ref name="Knudsen 1999" />
* Modeling base-pair covariation to detecting homology in database searches.<ref name="Eddy 1994" />
* pairwise simultaneous folding and alignment.<ref name="Rivas 2001" /><ref name="Holmes 2002" />

Different implementation of these approaches exist. For example, Pfold is used in secondary structure prediction from a group of related RNA sequences,<ref name="Knudsen 2003" /> covariance models are used in searching databases for homologous sequences and RNA annotation and classification,<ref name="Eddy 1994" /><ref name="Gardner 2010" /> RNApromo, CMFinder and TEISER are used in finding stable structural motifs in RNAs.<ref name="Yao 2006" /><ref name="Rabani 2008" /><ref name="Goodarzi 2012" />