Percentage sensitivity and positive predictive value (Sensitivity/PPV) for pairwise nucleotide-level alignments in the BRalibaseII benchmark.

We compared the performance of the TKFST model for progressive multiple alignment of RNAs against the performance of a grammar with a richer model of RNA structure (Stemloc [18]). Sensitivity is defined as and PPV is defined as , where TP is the number of true positives (correctly aligned residue pairs), FN is the number of false negatives (residue pairs that should have been aligned but were not) and FP is the number of false positives (residue pairs that were incorrectly aligned). These statistics are summed over all pairs of sequences in the multiple alignment; therefore, “Sensitivity” for pairwise residue alignments is equivalent to the Sum of Pairs Score or SPS [103]. “g2intron” is the RFAM entry Intron_gpII, containing domains V and VI of the Group II intron.