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Table 1 Comparison of RNAspa's accuracy versus that of other prediction programs

From: RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

Family Num. of seed seq. in Rfam Num. of datasets of ten Avg. sequence identity Avg. length and STD MCC
      RNA- subopt's first choice RNA- spa Stem- Loc pmMulti Fold-AlignM RNAcast
tRNA 1114 5 43% 71 ± 4 0.64 0.86 0.61 0.73 0.95 0.45 (3)
Tymo 28 2 68% 79 ± 3 0.76 0.93 0.98 0.72 0.94 0.92 (1)
SAM 71 5 62% 111 ± 15 0.59 0.66 0.38 0.64 0.53 0.62 (1)
Lysine 60 5 50% 179 ± 7 0.63 0.68 0.28 0.64 0.52 (1) 0.71 (1)
Purine 37 3 56% 96 ± 1 0.68 0.86 0.51 0.74 0.78 0.72 (1)
Cobalamin 171 5 46% 200 ± 27 0.38 0.40 0.12 no data no data 0.41
FMN 48 4 60% 135 ± 19 0.32 0.44 0.25 0.45 0.64 0.47 (1)
glmS 14 1 51% 159 ± 40 0.58 0.61 0.38 no data no data no data
  1. Each family was represented by several non-overlapping datasets (see third column). The MCC score is averaged among the datasets of each family. The number of datasets in which the program failed to produce an output appears in brackets. "no data" denotes that the program failed on all datasets. In some cases, StemLoc returns a consensus structure for only part of a dataset. Therefore, the MCC score reported here only reflects those sequences for which a structure was predicted. See [Additional File 5] for raw data.