Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars

Michael P. S. Brown, HNC

We instroduce a model based on stochastic context-free grammaers that con construct small subunit ribosomal RNA multiple alignements. The method takes into account both primary sequence and secondary structure basepairing interactions. We show that this method produces multiple alignbments of quality close to hand edited ones, and outperforms several other methods.


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