Background: Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of ...
Pseudoknots are widely occurring structural motifs in RNA. Pseudoknots have been shown to be functionally important in different RNAs which play regulatory, catalytic, or structur...
Jitender S. Deogun, Ruben Donts, Olga Komina, Fang...
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
We describe and demonstrate the effectiveness of a method of predicting protein secondary structures, sheet regions in particular, using a class of stochastic tree grammars as rep...