Small subunit ribosomal RNA modeling using stochastic context-free grammars.

We introduce a model based on stochastic context-free grammars (SCFGs) that can construct small subunit ribosomal RNA (SSU rRNA) multiple alignments. The method takes into account both primary sequence and secondary structure basepairing interactions. We show that this method produces multiple alignments of quality close to hand edited ones and outperforms several other methods. We also introduce a method of SCFG constraints that dramatically reduces the required computer resources needed to effectively use SCFGs on large problems such as SSU rRNA. Without such constraints, the required computer resources are infeasible for most computers. This work has applications to fields such as phylogenetic tree construction.