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Rna Secondary Structure Detection Programs With An Emphasis On Covariance Models, Justin Slotman
Rna Secondary Structure Detection Programs With An Emphasis On Covariance Models, Justin Slotman
Theses
RNA secondary structure prediction requires a different approach from traditional alignment methods. Functional RNAs often have their secondary structure better conserved than their primary structure. Covariance models, probabilistic models that utilize stochastic-context-free grammars, are one approach. CMs allow for homology to be detected where purely sequence-based methods would fail. A background on CMs is given, as well as a background of the major classes of non-coding RNAs (ncRNAs). Comparisons are made between some CM-using tools (the Infernal suite and CMfinder) and some other RNA secondary structure tools (CARNAC, miRNAminer, Pfold, Mfold) as well as between Infernal and the primary alignment …