Stochastic Context-free Grammars for Modeling RNA |
Common terms and phrases
1477 tRNA sequences 15 tRNA sequences alignment and folding alignment grammar alignment of tRNA anticodon calculate Computer context-free grammars SCFGs correct secondary structure current grammar database searching described discriminate tRNA sequences dynamic programming efficient EMBL Data Library estimate a SCFG Figure folded RNA sequence folded training sequences formal grammar forward-backward algorithm four nucleotides grammar is obtained graph grammars Harry Noller Haussler hidden Markov models initial grammar inside-outside algorithm internal nodes iteratively Krogh labeled tree length match nonterminals modeling RNA molecule Multiple Sequence Alignments NLL-score non-tRNA sequences nucleotides parse tree problems production probability quence reestimate regular grammar RNA secondary structures S₁ sequences cluster sequences with introns set of productions single grammar skip productions statistical model stochastic context-free grammars strings structure of RNA symbol terminal train SCFGs trained grammar training algorithm training examples tree-grammars tRNAs and non-tRNAs unaligned unfolded Watson-Crick base pairs XRNA Y₁ Z-score of tRNAs