Stochastic models such as hidden Markov models or stochastic context free grammars can fail to return the correct, maximum likelihood solution in the case of semantic ambiguity. T...
Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of effici...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fa...
Background: The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. How...
: Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life...
RNA pseudoknot prediction is an algorithm for RNA sequence search and alignment. An important building block towards pseudoknot prediction is RNA secondary structure prediction. T...