Base pair phylogenetically determined

Virtually all the nucleotides in DNA are in double-stranded secondary structures, but this is not true for RNA. In addition, RNA double helices may be less regular than B-DNA with some pyrimidine-pyrimidine base pairs and sometimes a looped-out base (Fig. 2.8). The determination of which nucleotides in an RNA molecule are in double-stranded structures involves both phylogenetic and biochemical data. In the phylo-... 

An updated recursive algorithm that minimizes free energy predicts 82.5% of phylogenetically determined base pairs from sequence in four small subunit rRNAs, four group I introns, three group II introns, and 41 tRNAs. The rRNAs and group II introns were folded in phylogenetically determined domains of no more than 500 nucleotides. 

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