The Application of Stochastic Context-free Grammars to Folding, Aligning and Modeling Homologous RNA Sequences |
Common terms and phrases
2BranchR anticodon ASCARIS SUUM CAENORHABDI CAENORHABDI.ELEG calculate CFGs chloroplast columns complete nucleotide sequence Computer CYANELCHLORO d-arm derivation Dirichlet Eddy & Durbin Escherichia coli estimate EUBACT folded RNA sequence folded sequences forward-backward algorithm grammar G Haussler helices Helix hidden Markov models HMMs homologous RNA initial grammar insect and echinoderm internal nodes iteratively Journal of Molecular Krogh lacking the D-domain length loop regions match nonterminals meta-nonterminals mitochondrial tRNAs Molecular Biology molecule multiple alignment NLL score non-tRNA sequences Nucleic Acids Research nucleotides obtain parameters parse tree predicted alignment productions rewrite protein pseudocounts pseudoknots RandomTRNA618 grammar reestimated regular grammar RNA family rRNA Sakakibara Sankoff SCFG Science Searls sequences from non-tRNA Sjölander Steinberg Stochastic context-free grammars stochastic grammars strings STRONGYLOCEN SUUN symbol T-stems terminal three trained grammars Tree-Grammar EM algorithm tRNA sequences tRNAs lacking TRUSTED alignment unaligned Waterman Watson-Crick base pairs Woese Y₁ Z score Z-score ZeroTrain Zuker