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Table 1 Comparing structure prediction performance of single sequence methods to pairSCFG. A comparison of the single sequence G s grammar and mfold to the pairSCFG.

From: Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

  Full Set 5S tRNA
Method Sens PPV Sens PPV Sens PPV
mfold v3.1.2 58 ± 2 56 ± 2 52 ± 3 49 ± 3 65 ± 3 62 ± 3
G s 48 ± 2 51 ± 2 39 ± 2 42 ± 2 61 ± 3 65 ± 3
self vs self G s 47 ± 2 42 ± 2 38 ± 3 35 ± 2 61 ± 3 55 ± 3
pairwise 67 ± 2 68 ± 2 56 ± 2 57 ± 2 85 ± 2 84 ± 2
  1. Using the pairSCFG to compare a sequence to itself (self vs self) shows that the pairwise grammar performs roughly equivalent to its single sequence counterpart in the absence of alignment information.