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Table 2 Results on the RNA STRAND-Rfam dataset

From: RNAalifold: improved consensus structure prediction for RNA alignments

RNA comment RIBOSUM RNAalifold Pfold KNetFold McC_mea
7SK   0.507 0.456 0.292 0.429 0.306
bicoid_3   0.949 0.840 n.a. 0.829 0.927
Corona_pk3 Pk 0.579 0.646 0.674 0.678 0.705
CPEB3_ribozyme Pk 0.756 0.756 0.663 0.756 0.612
Gammaretro_CES   0.983 0.948 0.983 0.935 0.983
Hammerhead_1   1.000 0.474 0.621 0.831 0.614
Hammerhead_3   1.000 0.960 1.000 1.000 1.000
HDV_ribozyme Pk 0.709 -0.018 0.784 0.388 0.396
IRES_c-myc   -0.004 0.079 0.286 -0.002 0.350
R2_retro_el   1.000 0.842 0.946 0.987 0.890
RNAIII   0.467 0.595 n.a. 0.479 0.830
RNase_MRP Pk 0.626 0.423 0.457 0.271 0.575
rne5   0.994 0.969 0.975 0.762 0.923
RydC Pk 0.466 0.562 0.608 0.466 -0.020
s2m   0.739 1.000 0.774 0.652 0.861
Telomerase-cil   1.000 0.937 0.921 1.000 0.953
Telomerase-vert pk 0.918 0.751 n.a. n.a. 0.820
Vimentin3   0.741 -0.016 0.184 0.771 0.629
Y   1.000 1.000 0.925 1.000 1.000
mean   0.759 0.651    0.703
mean knetfold 0.750 0.645   0.680 0.696
mean pfold 0.756 0.635 0.693 0.682 0.673
  1. Performance comparisons on the RNA STRAND-Rfam dataset. We list the MCC for different alignments. Best performance indicated in bold, n.a. means that data is not available due to length restrictions on the respective server, pk denotes structures that contain a pseudo-knot. As there are many pseudo-knotted structures in this dataset, KNetFold was used in the "Check pseudoknot" mode. The MCCs take into account the pseudo-knots.