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1477 tRNA sequences 15 tRNA 55 tRNA sequences alignment and folding alignment grammar alignment of tRNA anticodon calculate CAUCAGGGAAGAUCUCUUG Computer context-free grammars SCFGs correct secondary structure current grammar database searching discriminate tRNA sequences dynamic programming efficient EMBL Data Library 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 HMMs I. S. Mian initial grammar inn(S inside-outside algorithm internal nodes iteratively Krogh labeled tree length loop match nonterminals modeling RNA molecule Multiple Sequence Alignments non-tRNA sequences nucleotides parse tree problems production probability productions rewriting rules quence regular grammar RNA secondary structures sequences cluster sequences with introns set of productions single grammar Sjolander skip productions statistical model stochastic context-free grammars strings structure of RNA terminal train SCFGs trained grammar training algorithm training examples tree-grammars tRNAs and non-tRNAs Watson-Crick base pairs XRNA Z-score of tRNAs